Plant retroviral polynucleotides and methods for use thereof

ABSTRACT

Retroviral and retroviral-like polynucleotides, and vectors, proteins, and antibodies derived therefrom, that are useful for the introduction of genetic information into soybeans and other plant species.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No. 60/025,853, filed Sep. 9, 1996.

FIELD OF INVENTION

The present invention relates generally to retroviruses, pro-retroviral polynucleotides including pro-retroviral DNA, pro-retroviral-like DNA and more specifically to recombinant vectors derived therefrom for use in delivering genetic information to susceptible target plant cells.

BACKGROUND OF INVENTION

Repetitive DNA sequences are a common feature of the genomes of higher eukaryotes. Repetitive DNA family members in animals and higher plants are tandemly repeated or interspersed with other sequences (Walbot and Goldberg, 1979; Flavell, 1980), and may constitute more than 50% of the genome (Walbot and Goldberg, 1979). Estimates of the proportion of repetitive DNA in the soybean genome range from 36% to 60% (Goldberg, 1978; Gurley et al., 1979).

High copy-number repeats on the order of 10⁵ per haploid genome comprise only 3% of the soybean genome, whereas moderately repetitive sequences with copy-numbers in the 10³ range occupy 30-40% of the genome (Goldberg, 1978). Electron micrographic examination of these moderately repetitive sequences demonstrate that they average about 2 kb in length; however, 4% of those observed exceed 11 kb (Pellegrini and Goldberg, 1979).

Most of the highly repetitive sequences in higher eukaryotic genomes are relatively short and are organized in tandem arrays. For example, the chromosomal region adjacent to the centromere in higher eukaryotes is composed of very long blocks of highly repetitive DNA, called satellite DNA, in which simple sequences are repeated thousands of times or more. Tandemly repeated elements found in the soybean genome also include the ribosomal RNA (rRNA)-encoding genes. The approximately 800 rDNA copies are organized as one or more clusters of tandemly repeated 8-kb or 9-kb units (Friedrich et al., 1979; Varsanyi-Breiner et al., 1979).

The genomes of most higher eukaryotes also contain highly repetitive sequences that are distributed evenly throughout the genome, interspersed with longer stretches of unique (or moderately repetitive) DNA. These interspersed repetitive DNA elements are variable in length, are recognizably related but not precisely conserved in sequence, and exhibit relatively small repeat frequencies (Lapitan, 1992).

The dispersal pattern of interspersed repetitive elements in higher eukaryotic genomes has led to the suggestion that they are, or once were, transposable elements known as transposons (Flavell, 1986; Lapitan, 1992). Transposons are genetic elements that can move from one chromosomal location to another, without necessarily altering the general architecture of the chromosomes involved. The existence of transposons has only found general acceptance within the last few decades. Genes were originally believed to have fixed chromosomal locations that only change as a result of chromosomal rearrangements resulting from illegitimate crossing-over between incompletely homologous short sections of DNA. Then, in the late 1940's, McClintock's pioneering experiments with maize showed that certain genetic elements regularly “jump”, or transpose, to new locations in the genome (McClintock, 1984).

Transposable elements (TEs) reside in the genomes of virtually all organisms (Berg and Howe, 1989). TEs encode enzymes that bring about the insertion of an identical copy of themselves into a new DNA site. Transposition events involve both recombination and replication processes that frequently generate two daughter copies of the original transposable element; one remains at the parental site, while the other appears at the target site (Shapiro, 1983).

Two major classes of eukaryotic TEs have been identified, which are distinguished by their mode of transposition (Finnegan, 1989). Class I elements transpose via the creation of an RNA intermediate that is then re reverse-transcribed to create a DNA copy that integrates at the target site. This class includes several families of retroelements—retrotransposons and retroviruses—including the copia elements of Drosophila melanogaster, the gypsy/Ty3 family, the Ty1 element of yeast, and the mammalian immunodeficiency and Rous sarcoma (RSV) retroviruses. Each of these retroelement families are characterized in part by the presence of long terminal repeats (LTRs) at their borders (Finnegan, 1989); however, this class also includes non-LTR-containing elements like Cin4 from maize (Schwarz-Sommer and Saedler, 1988) and the mammalian L1 family (Hutchinson et al. 1989).

The copia elements in D. melanogaster possess long terminal direct repeats. There are more than 11 families of copia-like elements; the members of each are well-conserved and are located at 5 to 100 different sites in the Drosophila genome. These elements are about 5000 base pairs (bp) long, with long terminal repeats (LTRs) several hundred bp in length that vary in both sequence and length between families. At the termini of each element are short imperfect inverted repeats of about 10 bp.

Insertion of copia into a new chromosomal site is accompanied by replication of a 3-6 bp stretch of target DNA; the length, but not the sequence, of the direct repeats that consequently appear immediately before and after the element is the same for all members of the same family. Copia elements have one long open reading frame (ORF) that encodes proteins homologous to those of RNA tumor viruses: homologies to reverse transcriptase, integrase, and nucleic acid-binding proteins suggest that these proteins function to create an RNA intermediate for copia transposition.

Class II elements, like the Drosophila melanogaster P element (Engels, 1989; Rio, 1990) and the maize Ac/Ds element (Federoff, 1989), transpose directly to new sites without the formation of an RNA intermediate. P elements reside at multiple sites in the Drosophila genome and are 0.5 to 1.4 kb in length, bounded by perfect inverted repeats of 31 bp. They represent internally deleted versions of a larger element of about 3 kb called a P factor, which occurs in one or a few copies only in so-called “P strains” of Drosophila. Upon insertion into a new site in the genome, P elements create 8 bp duplications of the target sequence.

The Ac/Ds system in maize consists of Ds elements, which, like the P elements of Drosophila, are derived from a larger complete element called Ac. Ds elements exist in several different lengths, from 0.4 to 4 kb. Unlike P elements, Ds elements remain stationary within the chromosome unless an Ac element is also present. Ds elements contain perfect inverted repeats of 11 bp at their termini, flanked by 6-8 bp direct repeats of the target DNA. When a Ds (or Ac) element transposes, it leaves behind imperfect but recognizable duplications of the 6-8 bp target sequence.

As stated above, it appears likely that many interspersed repetitive DNA families are, or once were, transposons. In soybean, an interspersed repetitive DNA family whose structural characteristics clearly define it as a transposon family is the Tgm family. The Tgm family is related to the maize En/Spm transposons and consists of fewer than 50 members ranging in size from under 2 kb to greater than 12 kb (Rhodes and Vodkin, 1988).

Retroviruses are type I transposons consisting of an RNA genome that replicates through a DNA intermediate. Although the viral genome is RNA, the intermediate in replication is a double-stranded DNA copy of the viral genome called the provirus (Watson et al., 1987). The provirus resembles a cellular gene and must integrate into host chromosomes in order to serve as a template for transcription of new viral genomes (Varmus, 1982). New genomes are processed in the nucleus by unmodified cellular machinery.

The viral genome RNA looks like a cellular messenger RNA (mRNA), but does not serve as such following infection of a cell. Instead, an enzyme called reverse transcriptase (which is not present in the cell, but is instead carried by the virion) makes a DNA copy of the viral RNA genome, which then undergoes integration into cellular chromosomal DNA as a provirus. Integration of the viral DNA is precise with respect to the viral genome, but is semi-random with respect to the host cell genome, in that some sites are utilized more frequently than others (Shih et al., 1988). The integrated provirus serves as a template for production of new viral RNA genomes, which move to the cell membrane to assemble into virions. These bud from the cell membrane without killing the cell.

Retrovirus virions have icosahedral nucleocapsids surrounded by a proteinaceous envelope. The retroviral genome is diploid, and its general organization is well-known in the art. Typical retroviruses have three protein-encoding genes: gag (group-specific antigen) encodes a precursor polypeptide that is cleaved to yield the capsid proteins; pol is cleaved to yield reverse transcriptase and an enzyme involved in proviral integration; and env encodes the precursor to the envelope glycoprotein. A fourth type of retroviral gene, called tat, has been found at the 3′ end of the HTLV-I and -II genomes, which serves as a transcriptional enhancer. A few retroviruses have additional genes, such as onc, that give them the ability to rapidly induce certain types of cancer.

Retroviral genomes contain LTR sequences at both their 5′ and 3′ ends (Weiss, 1984). These sequences include signals needed for replication, transcription, and post-transcriptional processing of viral RNA transcripts. The LTRs are perfect direct repeats created by the addition of sequences (called U₅ and U₃, derived from the opposite ends of the viral genome) to each end of the viral genome during the creation of the double-stranded DNA intermediate. The U₅ region appears to be essential for initiation of reverse transcription and in packaging of viral transcripts (Murphy and Goff, 1988). The U₃ region contains a number of cis-acting signals for viral replication, and sequences responsible for much or all of the transcriptional control over viral genes.

Retroviral genomes also contain a primer binding site (PBS) near the 5′ end (Dahlberg et al., 1974). This sequence is complementary to the 3′ end of a cellular tRNA. The tRNA is stolen from the host cell during replication and serves as a primer for reverse transcription of the RNA genome soon after infection.

Once the provirus is integrated into cellular chromosomal DNA, it is stable and replicates along with the host cell DNA. Proviruses are never excised from the site of integration, although they may be lost as a result of deletions. Retrovirus infections usually do not harm the cell, and infected cells continue to divide, with the integrated provirus serving as a template to direct viral RNA synthesis.

Like all viruses, retroviruses have a specific requirement for interaction with a target cell-surface receptor molecule for infection. In all cases known (and suspected), this molecule is a protein that interacts specifically with a specific virion env protein. The best-studied of virion envelope protein-cell surface receptor interaction is that of HIV with the CD4 receptor on human T-cells (Dalgleish et al., 1984). The env protein appears to bind to a small region on the receptor not involved in cell-cell recognition or any other known function. Another retrovirus whose cellular receptor has been identified is Moloney murine leukemia virus (MMLV), which interacts with a cell surface protein that resembles a membrane pore or channel protein. Although the mechanism of interaction of many retroviruses is not yet well understood, it does appear that retroviruses interact with a wide variety of receptor types (Weiss, 1982).

Retroviruses have been studied intensely over the past several decades, mainly because of their ability to cause tumors in animals and to transform cells in culture. The ability of retroviruses to transform cells is based on at least two mechanisms. The first is that certain viruses have incorporated activated proto-oncogenes that upon mutation have acquired the ability to transform cellular growth. The second mechanism of transformation results from insertional mutagenesis upon integration of the viral genome. Because the viral LTRs have promoter and enhancer activities, insertion of an LTR sequence in either orientation adjacent to a cellular gene may lead to inappropriate expression of that gene. If the cellular gene is involved in regulation of cell growth, over- or under-expression or insertional mutagenesis of that gene may lead to uncontrolled growth of the cell.

Retroviral integration is thus potentially mutagenic. Integration of retrotransposons within exonic coding regions may inactivate those genes, while integration within introns or flanking regions may create novel regulatory patterns with significant developmental and evolutionary implications (McDonald, 1990; Robins and Samuelson, 1993; Schwarz-Sommer and Saedler, 1987; Weil and Wessler, 1990; White et al., 1994). Enhancers and trans(e activating sequences have been found in retroviral and retrotransposon LTRs (Boeke, 1989; Cavarec, et al, 1994; Choi and Faller, 1994; Lohning and Ciriacy, 1994; Mellentin-Michelotti et al., 1994; Varmus and Brown, 1989), and retrotransposon insertions between coding regions and enhancers disrupt gene expression (Cal and Levine, 1995; Georgiev and Corces, 1995; Geyer and Corces, 1992; White et al., 1994).

Element mobilization not only modifies target gene activity, it restructures genomic architecture (King, 1992, Lim and Simmons, 1994; McDonald, 1993; Shapiro, 1992). In fact, one of the major genomic differences between related taxonomic groups appears to be the identity and distribution of repetitive elements, not single-copy coding sequences (McDonald, 1993; Shapiro, 1992). White et al. (1994) have demonstrated that the flanking regions of many maize genes are embedded in sequences containing traces of retrotransposon DNA. Moreover, Palmgren (1994) has found that the BstI retroelement from maize encodes two conserved domains found in plant membrane H⁺-ATPases, suggesting that element acquisition of host sequences is not confined to vertebrate retroviruses.

McClintock (1984) has proposed that genetic variation, induced in part by transposable element-mediated insertional mutagenesis, is a directed response to conditions that create “genomic stress.” Many TEs and retroviruses preferentially insert in transcriptionally active regions of the genome (Engels, 1989; Sandmeyer et al., 1990; Varmus and Brown, 1989). The Ty1 retrotransposon in yeast can be activated by growth in suboptimal temperatures (Paquin and Williamson, 1988) and by exposure to radiation (McEntee and Bradshaw, 1988). Similar observations have been made in Drosophila (McDonald et al., 1988; Strand and McDonald, 1985), maize (McClintock, 1984), and soybean (Sheridan and Palmer, 1977).

In plants, TEs are activated during the induction of tissue culture (Hirochika, 1993; Peschke and Phillips, 1991) and may contribute to somaclonal variation observed for a number of higher plant species including soybean (Amberger et al., 1992; Freytag et al., 1989; Graybosch et al., 1987; Roth et al., 1989). In maize, the activation of transposable elements is correlated with changes in the pattern of DNA methylation that occur during induction of cultures (Brettell and Dennis, 1991; Kaeppler and Phillips, 1993; Peschke et al., 1991), providing a well-characterized basis for gene activation.

In plants, most transposon-like sequences appear to be extinct (Grandbastien, 1992). Although a number of plant species harbor these sequences (Flavell et al., 1992; Grandbastien, 1992; Voytas et al., 1992), active transposition has only been demonstrated or directly implicated in tobacco (Grandbastien, et al., 1989; Pouteau et al., 1994) and maize (Johns et al., 1985). RNA transcripts and cDNAs from transposons have been recovered from tobacco (Pouteau, et al., 1994; Hirochika, 1993) and maize (Hu et al., 1995), and transposable element-related proteins have been detected in maize (Hu et al., 1995).

The stable introduction of foreign genes into plants represents one of the most significant developments in a continuum of advances in agricultural technology that includes modern plant breeding, hybrid seed production, farm mechanization, and the use of agrichemicals to provide nutrients and control pests. Genetic engineering has been applied to many species in efforts to improve production efficiency and environmental conservation. Genetic engineering complements plant breeding efforts by increasing the diversity of genes and germplasm available for incorporation into crops and shortening the time required for the production of new varieties and hybrids, while also providing opportunities to develop new agricultural products and manufacturing processes.

The first transgenic plants were tobacco plants transformed with a chimeric neomycin phosphotransferase gene carried on the Ti plasmid of Agrobacterium tumefaciens (Horsch et al., 1984). Agrobacterium-mediated Ti plasmid transfer has proved to be an efficient, versatile method of plant transformation. The range of plant species amenable to genetic engineering using Agrobacterium is fairly large. In those systems where Agrobacterium-mediated transformation is efficient, it is the method of choice because of the facile and defined nature of the gene transfer.

Few monocotyledonous plants appear to be natural hosts for Agrobacterium, however, although transgenic plants have been produced in asparagus and transformed tumors have been observed in yam. Many commercially valuable crop species, such as cereal grains (e.g., rice, maize, and wheat) are not efficiently transformed by Agrobacterium, despite extensive efforts made in this direction. This appears to be due to differences in the wound response; those species recalcitrant to Agrobacterium-mediated transformation probably do not express the required appropriate wound response (Potrykus, 1991).

Physical methods of gene delivery have been developed in order to transform plants not susceptible to Agrobacterium. These methods include biolistic projection (“particle gun”), microinjection, electroporation, and lipofection (Potrykus, 1991). Most physical transformation experiments have utilized plant protoplasts as the recipient cells; however, other regenerable explants have been utilized, including leaves, stems, and roots. Many plant species have been successfully transformed with physical techniques, but some, notably legumes and cereals, have proved difficult to stably transform by these methods. The applicability of such physical methods to these plants is limited by the difficulties involved in regenerating plants from protoplasts, although some success in this regard has been achieved with some cereals and rice. Little success has been achieved with soybean or maize.

Little experimentation has been reported regarding the use of viral vectors for transformation of plants. Plant viruses exist in a variety of forms; they contain either DNA or RNA as their genetic material, have either rod- or polyhedral-shaped capsids, and can be transmitted either by insects, bacteria, or contact with wounded regions (Robertson, et al., 1983). Most known plant viruses contain single (+) strand RNA as their genetic material. (+) strand plant viruses can further be divided into those which possess a single RNA chain and those which have several RNA chains, each necessary for viral infectivity and which are separately encapsulated into separate virions. Cowpea mosaic virus, for example, contains two RNAs, one encoding several proteins including terminal protein and a protease, with the other chain encoding capsid proteins. There also exist segmented double-strand RNA plant viruses. The best-known of these is wound tumor virus (WTV) which contains 12 different segments and which can replicate in either insect or plant cells.

There are fewer plant DNA viruses. Only two known classes exist, one of which contains double strand DNA and which has a polyhedral capsid. The best understood of this class is cauliflower mosaic virus (CMV). The second class of DNA plant viruses are the geminiviruses that consist of paired capsids held together like twins with each capsid containing a circular single-stranded DNA of about 2500 nucleotides. In some cases, the two paired genomes are identical, while in other cases, the two bear almost no sequence relationship.

Early work with a DNA virus showed that a small bacterial antibiotic resistance gene integrated into such a virus could spread systemically throughout infected plants and confer resistance (Brisson, et al., 1984). It has been suggested that the small size of DNA viral genomes is prohibitory to the wide application of such vectors as useful transforming agents in plants. However, little has been done to follow up on this work.

Even less work has been performed in plants regarding the application of genetic engineering to the far larger group of plant RNA viruses (Ahlquist et al., 1987; Ahlquist and Pacha, 1990). It has been suggested that because the viral RNA does not integrate into the host genome, and is excluded from the meristems and offspring, the usefulness of such RNA viruses in plant transformation is limited at best (Potrykus, 1991).

SUMMARY OF THE INVENTION

In one aspect, the present invention provides retroviral and retroviral-like polynucleotides derived from a plant wherein such polynucleotides are capable of integration into the genome of a plant cell. The invention is also directed to other plant retroviral or retroviral-like polynucleotides obtainable by hybridization under stringent conditions (see, e.g., Sambrook et al.) with the retroviral or retroviral-like polynucleotides expressly disclosed herein. Also within the scope of this aspect of the invention are regulatory sequences comprising, for example, plant retroviral long terminal repeat (LTR) sequences that may be operably linked to a gene so as to modulate expression of the linked gene.

In a second aspect, the invention is directed to plant retroviral or retroviral-type elements capable of targeted integration into a specific region in the plant genome and further to methods for accomplishing such integration.

In a third aspect, the present invention is directed to vectors containing all or part of a regulatory sequence derived from a plant retrovirus or retrovirus-like polynucleotide, and to vectors comprising all or part of the retroviral or retroviral-like genome and a heterologous gene.

In a fourth aspect, the invention is directed to vectors containing one or more plant retroviral or retroviral-like regulatory sequences operably linked to a heterologous gene. A heterologous gene in the context of the present application refers to a gene or gene fusion or a part of a gene derived from a source other than the plant pro-retrovirus, or a cDNA, or a plant retroviral gene under the regulatory control of a promoter other than its natural promoter.

In a fifth aspect, the invention is directed to isolated purified proteins encoded by the polynucleotides disclosed herein, and to analogs, homologs, and fragments of such proteins that retain at least one biological property of the proteins.

In a sixth aspect, the invention is directed to isolated purified proteins produced by expression of a heterologous gene using the vectors of the present invention.

In a seventh aspect, the invention is directed to methods for using vectors comprising all or part of a plant proretroviral or retroviral genome and vectors comprising plant retroviral regulatory sequences operably linked to a heterologous gene to introduce a heterologous gene or a regulatory element into a plant genome, wherein the expression product of the gene comprises a polypeptide or an antisense RNA and wherein the regulatory element is a transcriptional regulatory element.

In an eighth aspect, the invention is directed to a plant retrovirus comprising a plant retroviral or retroviral-like polynucleotide, a capsid, and an envelope.

In a ninth aspect, the invention is directed to methods for producing a plant retrovirus, in which the plant retroviral polynucleotide is packaged in a capsid and envelope, preferably through the use of a packaging cell line, but alternatively by use of other vector systems or by in vitro constitution of the retroviral capsid and envelope.

In a tenth aspect, the invention is directed to plant cells that have been transformed by transduction of a plant retroviral polynucleotide or transformed by a plant retrovirus comprising a heterologous gene according to the methods of the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the DNA sequence of the oligonucleotide used as a primer in the polymerase chain reaction that generated the plant pro-retrovirus SIRE-1 cDNA Gm776 (SEQ ID NO:1). The 5′ and 3′ ends of the oligonucleotide are indicated, and degenerate sites (wherein the oligonucleotide mix contained equal proportions of two nucleotides at a given site) are re indicated in parentheses.

FIG. 2 presents the nucleotide sequence of the SIRE-1 cDNA Gm776 (SEQ ID NO:2). The regions corresponding to the oligonucleotide primer used to amplify the cDNA are underlined.

FIG. 3 depicts a restriction map of the SIRE-1 Gm776 cDNA sequence.

FIG. 4 shows a statistical analysis of sequence similarities between Gm776 and retrotransposons from A. thaliana and Saccharomyces cerevisiae.

FIGS. 5A and 5B set forth the DNA sequences of oligonucleotides (SEQ ID NOS: 12-24) utilized in sequencing Gm776 and the 2.4 kb SIRE-1 cDNA.

FIG. 6 (Parts A-C) sets out the nucleotide sequence (SEQ ID NO: 3) of the 2.4 kb SIRE-1 cDNA isolated from a lambda gt11 soybean cDNA library.

FIG. 7 depicts a restriction map of the 2.4 kb SIRE-1 cDNA.

FIG. 8 depicts the organization of the 2.4 kb SIRE-1 cDNA.

FIG. 9 shows a comparison of the predicted SIRE-1 CX₂CX₄HX₄C (SEQ ID NO: 60) nucleic acid-binding site sequences (SEQ ID NO: 4 and SEQ ID NO: 61) with the amino acid sequences of those in other nucleocapsid proteins (SEQ ID NOS: 62-68).

FIG. 10 shows a comparison of the predicted amino acid sequence (SEQ ID NO: 5) of the putative SIRE-1 protease domain with the amino acid sequences of other retroelement proteases ( SEQ ID NOS: 69-75).

FIG. 11 shows an alignment of the RNA sequence (SEQ ID NO: 6) of the putative SIRE-1 primer binding site to the 3′-end of soybean tRNA^(met−1) (SEQ ID NO: 76). Identity between the sequences is indicated by a vertical line (|).

FIG. 12 shows a sequence alignment between the 3′-termini of the putative 5′ LTR of SIRE-1 (SEQ ID NO: 7) and the 5′ LTR of the potato retrotransposon Tst1 (SEQ ID NO: 77). Identity between the sequences is indicated by a vertical line (|).

FIG. 13 (Parts A-E) sets out the DNA sequence (SEQ ID NO: 8) of the 4.2 kb fragment of the SIRE-1 genomic clone isolated from a lambda bacteriophage FIX II soybean genomic library.

FIG. 14 depicts the organization of the 4.2 kb SIRE-1 genomic fragment.

FIG. 15 (Parts A-B) shows the predicted amino acid sequence encoded by the SIRE-1 open reading frames ORF1 (single underline) (SEQ ID NO: 9) and ORF2 (SEQ ID NO: 59) (double underline) encoded by the 4.2 kb SIRE-1 genomic fragment. The sequences formed by stop codons are also shown (SEQ ID NO: 85 and SEQ ID NO:86).

FIG. 16 shows the predicted amino acid sequence (SEQ ID NO: 84) encoded by the SIRE-1 open reading frame ORF2. The putative signal peptide sequence (residues 22-43) and hydrophobic anchor sequence (residues 511-531) are underlined.

FIG. 17 shows a comparison of the predicted amino acid sequence (SEQ ID NO: 11) of the SIRE-1 ORF1 with the C-terminal region of the copia RNase H polypeptide (SEQ ID NO: 78). Vertical lines (|) indicate identity between the sequences, whereas conservative and semi-conservative substitutions are indicated by (:) or (.) respectively.

FIG. 18 shows a restriction map of the SIRE-1 genomic clone isolated from a λ bacteriophage FIX II soybean genomic library. The 5′ and 3′ ends of the insert are at the left and right, respectively. The numbers above and below the schematic indicate the approximate lengths of the restriction fragments. The restriction endonuclease recognition sites are indicated by single letter codes: H represents a Hind III site; X represents an Xba I site; and N represents a Not I site. The boxed regions of the schematic represent open reading frames encoding SIRE-1 proteins: int represents the integrase domain; RT represents the reverse transcriptase domain; RH represents the Ribonuclease H domain; and env represents the envelope protein domain. The rightmost (open) box represents the 3′ soybean flanking region.

FIG. 19 shows the DNA sequences (SEQ ID NOS: 25-38) of oligonucleotide primers used to sequence the 4.2 kb genomic fragment. The numbering in the second column indicates the position of the primer sequence with reference to the predicted sense strand of the genomic pG fragment. Also shown are M13/pUC forward (SEQ ID NO: 12) and reverse oligonucleotide sequences (SEQ ID NO: 14).

FIG. 20 shows the results of a computer analysis performed on the predicted ORF2 amino acid sequence (SEQ ID NO: 55) using the computer program NNpredict (Kneller et al. 1990).

FIG. 21 shows a nucleotide sequence comparison among the SIRE-1 3′ LTR (LTR2) (SEQ ID NO: 58) and the gag R1 (SEQ ID NO: 57) and R2 (SEQ ID NO: 56) regions. The numbers following the sequence designations indicate the respective locations of the regions within the SIRE-1 4.2 kb genomic fragment.

FIG. 22 (Parts A-C) depicts a nucleotide sequence comparison between Gm776 (SEQ ID NO: 2) and the 2.4 kb SIRE-1 cDNA (SEQ ID NO: 3). The Gm776 DNA sequence is in reverse orientation (i.e., in the 3′ to 5′ orientation) to the 2.4 kb cDNA sequence.

FIG. 23 shows the predicted amino acid sequence (SEQ ID NO: 83) of ORF2. The putative hydrophobic transmembrane regions are indicated by a single underline. The predicted coiled-coil regions are indicated by a double underline. The proline rich region is indicated by a dotted underscore. The predicted α-helical regions are indicated in boldface type. The potential SU/TM cleavage sites are indicated by boxes.

FIG. 24 depicts an agarose gel electrophoretic analysis of restriction endonuclease digestion of the SIRE-1 λFIXII genomic DNA by Hind III. Lane 1 contains λ DNA size markers. Lane 2 contains the SIRE-1 λFIXII genomic DNA digested by Hind III. The relative lengths of the Hind III fragments are indicated by the numbers (e.g., 2.1 H is a 2.1 kb Hind III fragment).

FIG. 25 shows a schematic representation of the results of restriction endonuclease digestion and Southern hybridization analyses of the SIRE-1 genomic clone. The length and nature of each fragment is indicated by the alphanumerical designation at the left (e.g., 1.5H is a 1.5 kb Hind III fragment). The fragment(s) recognized by each probe (i.e., env, gag, LTR) are indicated by the arrows.

FIG. 26 presents the result of a restriction endonuclease digestion and Southern hybridization analysis of the SIRE-1 genomic clone. The SIRE-1 genomic clone was digested with Sac I and Hind III. The length of the hybridizable fragments is indicated to the left. The Southern hybridization was performed with a radioactively labeled env probe derived from the 4.2 kb Xba I fragment.

FIG. 27 presents a schematic of the pEG4.1 vector construct. The 4.1 kb SIRE-1 insert is indicated by the thick bolded clockwise arrow.

FIG. 28 depicts the result of restriction endonuclease digestion and Southern hybridization analysis of the pEG4.3 vector construct comprising the 4.3 kb SIRE-1 Hind III fragment. The Southern hybridization was performed using a radioactively labeled gag probe derived from the 4.2 kb SIRE-1 Xba I fragment.

FIG. 29 presents a schematic of the pEG4.3 vector construct. The 4.3 kb SIRE-1 insert is indicated by the thick bolded clockwise arrow.

FIG. 30 presents the sequences (SEQ ID NOS: 39-49) of oligonucleotide primers utilized in the sequencing of the 4.1 kb and 4.3 kb SIRE-1 Hind III fragments contained in pEG4.1 and pEG4.3, respectively. The lower-case c following a primer designation indicates that the primer was utilized for sequencing the (−) strand of the insert. Also shown are PUC forward (SEQ ID NO: 12) and reverse (SEQ ID NO: 14) oligonucleotide sequences.

FIGS. 31(a)-(c) presents the nucleotide sequence (SEQ ID NO: 50) of the SIRE-1 genomic clone derived from the sequences of the 4.1 and 4.3 kb SIRE-1 Hind III fragments. The first 321 nucleotides of the sequence are derived from the 31 terminus of the 4.3 kb Hind III fragment, and the remaining sequence is derived from the 4.1 kb Hind III fragment. The Hind III restriction endonuclease recognition site is indicated in boldface (nt 322-327).

FIG. 32 presents the amino acid sequence (SEQ ID NO: 51) of the predicted open reading frame encoded by the combined nucleotide sequences of the 4.3 kb and 4.1 kb Hind III fragments of the SIRE-1 genomic clone.

FIG. 33 presents a comparison of the predicted amino acid sequence (SEQ ID NO: 52) of the SIRE-1 int domain with the integrase domain of the Opie-2 retroelement (SEQ ID NO: 79) from maize. The amino acid residues constituting the HHCC and D(10)D(35)E conserved motifs are presented in boldface. A (.) represents a gap in the sequence required for optimal alignment. A (|) represents identity between the residues. A (:) represents similarity between the residues.

FIG. 34 presents a comparison of the predicted amino acid sequence (SEQ ID NO: 53) of the SIRE-1 reverse transcriptase (RT) domain and the reverse transcriptase domain of the Opie-2 retroelement from maize (SEQ ID NO: 80). The regions corresponding to conserved retroelement RT domains are presented in boldface. A (|) represents identity between the residues. A (:) represents similarity between the residues.

FIG. 35 presents a comparison of the predicted amino acid sequence (SEQ ID NO: 54) of the SIRE-1 Ribonuclease H (RH) domain and the Ribonuclease H domain of the Opie-2 retroelement from maize (SEQ ID NO: 81). The conserved DEDD motif is indicated by boldface. A (|) indicates identity between the residues. A (:) indicates similarity between the residues. A (.) indicates a gap in the sequence required for optimal alignment.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides novel plant retroviruses, proretroviruses, proretroviral polynucleotides, proretroviral DNAs, proretroviral-like polynucleotides and plant retroviral derivatives that are useful for genetic engineering in plants. More particularly, the plant retroviruses, proretroviruses, proretroviral polynucleotides, proretroviral DNAS, proretroviral-like polynucleotides, and plant retroviral derivatives derived therefrom are useful for: introducing a heterologous DNA of interest into plant cells where the peptide or polynucleotide encoded by that sequence will be expressed; for introducing a DNA sequence of interest into plant cells where the RNA encoded by that sequence is complementary (antisense) to an endogenous plant polynucleotide; for introducing a DNA sequence into a plant cell where that sequence becomes integrated into a plant genome; for integrating gene regulatory elements such as transcriptional regulatory sequences into a plant genome; and for identifying the location of such integrations.

The invention provides vector constructs comprising plant proretroviral polynucleotides, proretroviral DNAs, proretroviral-like polynucleotides, fragments thereof, and retroviral derivatives derived therefrom that are useful for: expressing desired proteins in target plant cells, for example, proteins that confer enhanced growth, disease resistance, or herbicide tolerance to plant cells, or to express “antisense” RNA complementary to an endogenous plant polynucleotide.

The invention also provides methods for: producing a plant retroviral vector; using a plant retroviral polynucleotide to identify genetic loci and to characterize the function of a gene within a plant genome; introducing mutations into a plant genome or disrupting an endogenous plant gene (“knockout”); and inserting genes or gene regulatory elements into genomic loci of plants.

The following examples are illustrative of certain embodiments of the present invention but are not to be construed as limiting thereof.

Example 1 describes the isolation and characterization of the SIRE-1 cDNA.

Example 2 describes the isolation and characterization of a full-length SIRE-1 clone from a soybean genomic library.

Example 3 describes the analysis of transcriptional activity from the SIRE-1 pro-retrovirus in soybean and other plants.

Example 4 describes the detection of SIRE-1 retrovirally encoded protein expression in plant tissues by Western blot analysis.

Example 5 describes the in vitro production of polypeptides from SIRE-1-encoded mRNAs.

Example 6 describes the use of SIRE-1 in non-replicative transduction of plant cells.

Example 7 describes methods and products for production of plant retrovirus packaging cells.

Example 8 describes methods for transduction of plant retroviral polynucleotides into plant cells.

Example 9 describes the use of SIRE-1 as a gene transfer vector.

Example 10 describes the use of SIRE-1 to induce and tag mutations in plant genomes.

Example 11 describes the modification of SIRE-1 to effect directed integration at a specific locus in a plant genome.

Example 12 describes the use of SIRE-1 and flanking DNA sequences to determine the site of SIRE-1 insertion in the soybean genome.

EXAMPLE 1 Isolation and Characterization of SIRE-1 cDNA

The initial characterization of the SIRE-1 retroviral DNA was based on the fortuitous recovery and analysis of a 776-bp DNA fragment (Gm776) generated by the polymerase chain reaction (PCR) in an attempt to amplify soybean DNA coding for a cytokinin biosynthetic enzyme (Laten and Morris, 1993). Amplification of either total DNA (from etiolated plumules of Glycine max cv Williams, isolated by the method of Doyle and Doyle, 1990) or nuclear DNA (from G. max cv Wayne, isolated by the method of Hagen and Guilfoyle, 1985) with the single 22-nt oligonucleotide primer (FIG. 1; SEQ ID NO: 1) generated high levels of Gm776. The amount of Gm776 generated in each PCR amplification suggested that SIRE-1 is a member of a multicopy DNA family, and the absence of additional bands suggested that the family is relatively conserved.

Hybridization and restriction digest analyses were performed to characterize the element size of the SIRE-1 family. Soybean genomic DNA was cleaved with BaRHI, EcoRI, HaeIII, HindIII, HpaI, and MboI, respectively, electrophoresed through 0.7-6 agarose, and blotted to a nylon membrane. The blot was hybridized with radiolabeled Gm776 cDNA in 0.05 M Tris, 1 M NaCl pH 7.5 in 50% formamide at 42° C., washed, and exposed to autoradiography (Southern, 1975). These analyses indicated that the SIRE-1 family is composed of several hundred, non-tandem, highly homogeneous copies, each in excess of 10.6 kb in length.

XbaI linkers were ligated to agarose gel electrophoresis (AGE)-purified Gm776 (modified Gm776) (Sambrook et al., 1989; Titus, 1991). The modified Gm776 DNA was extracted with phenol/chloroform and chloroform, ethanol- precipitated, and redissolved in 10 mM Tris-HCl, 1 mM EDTA, pH 7.6. pUC19 was linearized with XbaI and dephosphorylated (Sambrook et al., 1989). Linearized pUC19 DNA and the modified Gm776 DNA insert with the ligated XbaI linkers were ligated, and DH5-α cells were transformed with the ligation products. Transformants were identified by resistance to the antibiotic ampicillin (amp^(r)), and the presence of plasmids containing the insert in the amp^(r)lac⁻ colonies was determined by hybridization with ³²P-labeled probe synthesized from PCR-amplified, PAGE-purified Gm776 DNA. Plasmid DNA from colonies giving positive hybridization signals was isolated by alkaline lysis (Sambrook et al., 1989).

The recovered pGm776 plasmid DNA was sequenced by dideoxynucleotide chain termination using Sequenase 2.0 (U.S. Biochemical, Cleveland, Ohio) and plasmid-specific and insert-specific primers according to the manufacturer's instructions (FIG. 2, SEQ ID NO: 2; FIGS. 5A and B, SEQ ID NOS: 12-24). Sequence analysis suggested that SIRE-1 is a member of the copia/Tyl retrotransposon family. SIRE-1 sequences were subsequently detected by hybridization studies using the Gm776 cDNA probe in the genome of G. max cv Williams, in several different cultivars, and in the ancestral species, Glycine soja. The copy number of the element among these sources varies from a few hundred to over a thousand. The variation in copy number, especially among domestic cultivars, suggested that the family remains active, e.g., capable of replication and transposition. The homogeneity of the sizes of the SIRE-1 family members also suggested that most are relatively young and have not had time to accumulate a large number of mutations.

The nucleotide and all six possible peptide translations of the Gm776 sequence were compared to sequences in the GenBank and EMBL databases (Devereux et al. 1984). No closely related sequences were revealed in these searches. However, statistical analyses of sequence similarities between Gm776 and retrotransposons from A. thaliana and Saccharomyces cerevisiae were performed using the Gap computer program (Devereux et al. 1984), and revealed lengthy, albeit weak, sequence similarities. The results of the analyses are set forth in FIG. 4. Column (a) in FIG. 4 denotes the nucleotide ranges within Gm776 that exhibit sequence similarities to other retrotransposon elements, and column (b) denotes the retrotransposon elements that exhibit nucleotide sequence homology to the sequences in column (a). Column (c) shows the percentage identity between the sequence ranges in columns (a) and (b), with gap weights of 3.0 for Ta1 and 2.0 for Ty1 and a gap length weight of 0.3. Two overlapping 300-plus bp regions between nt 150 and 670 of Gm776 exhibit over 50% identity to adjacent regions overlapping the Ta1 RNA binding domain. The alignments include seven gaps in each sequence, averaging 2.5 bp per gap.

When the six potential Gm776 translation sequences were compared to the sequence of the Ta1 polyprotein in the region of DNA similarity, no similarities were observed. However, 51% of the nucleotides between bp 390 and 630 of Gm776 are identical to a sequence within the reverse transcriptase gene of the Saccharomyces cerevisiae retrotransposon Tt1. The alignment requires five gaps averaging 2 bp per gap. There is no significant similarity between any of the six potential Gm776 translation sequences and the corresponding region of the S. cerevisiae reverse transcriptase. Sequence comparisons with several other plant transposons, including the copia-like elements Tntl from tobacco (Grandbastien et al. 1989), Tstl from potato (Camirand et al. 1990), and PDR1 from pea did not reveal significant similarities.

Column (d) in FIG. 4 denotes the “qualities” of sequence matches denoted in column (c), and column (e) denotes the qualities and standard deviations of randomized sequence alignments of the same lengths and base compositions. Column (h) represents the probabilities (P) for normal distribution calculated using the equation P=0.3989e^(−(x2/2)) where x=(Q-meanQ)/S.D. The results indicate that the derived similarities are quite significant, especially as approximately 150,000 nucleotides in 30 transposons were analyzed.

A soybean cDNA lambda gt11 bacteriophage library (Clontech) was screened for the presence of SIRE-1 cDNAs by hybridization methods well-known in the art (Sambrook et al. 1989). The radiolabeled probe was generated from the pGm776 plasmid using the Multiprime DNA Labeling kit (Amersham, Arlington Heights, Ill.). Three phage plaques (out of 6,000 screened) showed positive hybridization signals and were isolated by limiting dilution and rescreening. Recombinant phage DNA from one of the clones was isolated from plate lysates (Sambrook et al., 1989) and purified on a Qiagen-100 column as recommended by the manufacturer (Qiagen, Chatsworth, Calif.). The clone contained a 4.0 kilobasepair (kb) insert that was transferred from the phage vector to pUC18 as follows. The purified phage DNA was digested with EcoRI, extracted with phenol/chloroform and chloroform, ethanol precipitated, and redissolved in 10 mM Tris-HCl, 1 mM EDTA, pH 7.6. pUC18 was linearized with EcoRI and dephosphorylated (Sambrook et al., 1989). Linearized pUC18 DNA and the 4.0 kb EcoRI DNA insert were ligated, and DH5-α cells were transformed with the ligation product. Transformants were identified by resistance to the antibiotic ampicillin (amp^(r)), and the presence of plasmids containing the insert in the amp^(r)lac⁻ colonies was determined by hybridization with ³²P-labeled probe synthesized from PCR-amplified, gel-purified Gm776 DNA.

Plasmid DNA from colonies giving positive hybridization signals was purified over a Qiagen-100 column as described above. Initially, digestion of plasmid DNAs with EcoRI generated insert fragments of 2.4 and 1.6 kb. Only the former hybridized to the Gm776 probe. However, the recombinant plasmid isolated for sequencing contained only the 2.4 kb SIRE-1 fragment, and re-isolation of the original construct proved difficult. The 2.4 kb cDNA insert was sequenced by dideoxynucleotide chain termination using Sequenase 2.0 (U.S. Biochemical, Cleveland, Ohio) and plasmid-specific and insert-specific primers according to the manufacturer's instructions, and was found to be 2389 bp in length (FIG. 6; SEQ ID NO: 3; GenBank Accession No. U22103).

The cDNA was found to contain an uninterrupted 617-codon open reading frame (ORF) beginning at nucleotide (nt) 236 (FIGS. 6 and 8; SEQ ID NOS: 8,9). A second 87-codon ORF begins at nt 2155 and continues through the end of the truncated fragment (FIGS. 6 and 8). The ATG codon at nt 236 is the fourth ATG in the sequence. Extended leader regions with ATGs upstream of the actual translational start site are not unknown among retroelement mRNAs (Varmus and Brown, 1989). In the SIRE-1 cDNA (SEQ ID NO: 8), the first ATG at nt 28 is followed immediately by a stop codon, and initiations at the two other upstream ATGs each may produce only a dipeptide. It has been suggested that 40S ribosomal subunits can reinitiate and resume scanning beyond very short, upstream ORFs (Kozak, 1991). The ATG at nt 236 is closely followed by another in-frame ATG at nt 242. The latter is actually in a more representative context for translational initiation than is the former (Heidecker et al., 1986).

The ORF1 of SIRE-1 (FIGS. 6, 8, and 9; SEQ ID NO: 9) contains three regions that are characteristically highly conserved among retroviral and retrotransposon polyproteins (Katz and Jentoft, 1989; Varmus and Brown, 1989). The first two are CX₂CX₄HX₄C (SEQ ID NO: 60). (where C represents cysteine, H represents histidine, and X denotes any amino acid) nucleic acid-binding motifs (i.e., CCHC boxes) found in retroviral and retrotransposon nucleocapsid (NC) proteins encoded by gag, and the third is a catalytic domain (LDSG: lysine-aspartic acid-serine-glycine) characteristic of prot-encoded aspartic proteases that cleave retroelement polyproteins.

In a few characterized retroelements, the CCHC boxes in the gag region are repeated. The repetition of the CCHC boxes in SIRE-1 is unique in that the boxes are separated by 189 codons, rather than by just a few codons as in other retroelements (FIG. 8). As NC proteins are generally less than 100 amino acids in length, it is possible that the SIRE-1 boxes are expressed in two distinct proteins.

Both SIRE-1 CCHC boxes are flanked by highly basic regions, especially the region between the boxes: seven of nine amino acids that precede the downstream box are lysine or arginine. This is characteristic of retroelement NC proteins, which are highly basic and are dominated by polar amino acids. Although the boundaries of the SIRE-1 NC proteins are not yet defined, CCHC boxes are generally found near the carboxy-terminus. The putative NC protein encompasses roughly amino acids 260 to 525. This region is highly basic (23%) and very polar (62%). Sequence comparisons between the SIRE-1 protease peptide sequence and those of other retroelements firmly places SIRE-1 in the copia/Ty1 family (FIGS. 9 and 10).

Retroelement (−) strand replication is usually primed by a host tRNA, often the initiator tRNA. A 22-nt primer binding site (PBS) complementary to the 3′ end of soybean tRNA^(met−1) (SEQ ID NO: 76) lies upstream of the SIRE-1 ORFs, between nucleotides 180 and 201 (SEQ ID NO: 6). See FIG. 11. Retroelement PBSs are generally located adjacent to the 5′-LTR (Boeke, 1989). Two bases separate the 5′ end of the SIRE-1 PBS from the dinucleotide CA, found at the 3′ end of nearly every LTR. The sequence of the downstream LTR from a genomic clone (see Example 2) confirms that this dinucleotide marks the end of the LTR. The a putative SIRE-1 LTR (SEQ ID NO: 7) shows significant homology to the terminal 17 nt of the 5′ LTR of the potato retrotransposon Tst1 (SEQ ID NO: 77). See FIG. 12.

An unusual feature of SIRE-1 is the presence of a 95-bp, nearly tandem, direct repeat between nt 2096 and 2299 (FIG. 6; SEQ ID NO: 3). The repeats are separated by 3 bp. The upstream member has an 11-bp insertion that is absent in the downstream member. Otherwise, the sequences are 95% identical. The 5% divergence makes it very unlikely that the duplication was created during the cloning process.

The 2.4 kb cDNA sequence was aligned to the corresponding region of Gm776, and it was found that the amplified fragment lies completely within the gag region of the 2.4 kb fragment, and that the two sequences differ by only 2% (FIG. 22). Of the 13 bp differences, seven retain the same amino acid. Of the remaining six, three result in the substitution of one non-polar amino acid for another—isoleucine for phenylalanine, isoleucine for valine, and leucine for methionine—and two are substitutions of threonine by isoleucine. The last substitution generates a stop codon in Gm776. Among the amino acid changes, only the threonine to isoleucine substitution is not considered to be a conservative replacement. The predominance of silent and conserved substitutions strongly suggests that the differences reflect the slightly diverged, evolutionary relationship between two SIRE-1 family members.

EXAMPLE 2 Isolation and Characterization of the SIRE-1 Genomic Clone

Oligonucleotide primers (FIG. 5B; SEQ ID NOS: 15-24) were utilized in PCR to amplify fragments from the gag and pol regions and from part of the adjacent LTR of the 2.4 kb cDNA clone. These amplified fragments and synthetic oligonucleotides (FIG. 5) were used to generate gag- and LTR-specific radiolabeled probes. A λFIXII soybean genomic library (Stratagene, La Jolla Calif.) was probed with radiolabeled SIRE-1 gag probes and positively-hybridizing plaques were purified by limiting dilution screening (Sambrook et al., 1989). DNA was prepared from phage recovered from liquid culture (Burmeister and Lehrach, 1996).

The phage DNAs containing the putative SIRE-1 genomic clones were digested with the restriction endonuclease Not I to release the DNA inserts from the phage. The largest DNA inserts obtained thereby were digested with Xba I, and Southern blots of the digested DNAs were probed with an end-labeled, LTR-specific oligonucleotide to identify clones carrying two LTRs. Analyses of one clone yielded two hybridizing bands, indicating that this clone contained two LTRs and was a probable source of a full-sized, intact copy of SIRE-1. The purified phage DNA containing the full-length SIRE-1 genomic clone was deposited with the American Type Culture Collection, 12301 Parklawn Drive, Rockville Md. 20852 on Aug. 12, 1997 (ATCC accession number 209200) in accordance with the Budapest Treaty requirements.

Restriction endonuclease digestion of the phage DNA with Xba I yielded three fragments of 8.5, 6.5 and 4.2 kb. Southern hybridization of the electrophoretically separated fragments with a radioactively labeled 2.4 kb SIRE-1 cDNA probe revealed that the SIRE-1 2.4 kb cDNA sequence extends across the 12.5 kb and 4.2 kb Xba I fragments.

The fragments were each subcloned into a PSPORT-1 plasmid (Life Technologies, Gaithersburg Md.) for automated DNA sequencing. Some of these subclones were unstable, but the one carrying the 4.2 kb Xba I fragment that hybridized to the LTR probe, but not to the gag probe, displayed no evidence of rearrangement. Both strands of this 4.2 kb clone were sequenced on ABI Prism 377 DNA sequencers using pUC universal primers and the oligonucleotide primers listed in FIG. 19 (SEQ ID NOS: 25-38). This sequence (FIG. 13; SEQ ID NO: 8) is made available as GenBank Accession number U96295.

The 4.2 kb XbaI fragment encompasses the 3′ end of the genomic clone and contains the distal 3.7 kb of SIRE-1 along with 538 bp of presumably single-copy flanking DNA (FIG. 14). Analysis and predicted translation of the SIRE-1 genomic sequence revealed the presence of two ORFs (FIG. 14). The first, ORF1 (SEQ ID NO: 9 and 11; See FIG. 15A) extends from nucleotide (nt) 1 to nt 191, and is clearly the 3′ end of a retroelement ribonuclease H (RH)-encoding sequence. The 3′ terminus of the SIRE-1 RH coding region exhibits significant amino acid sequence homology (i.e., 53% identity and 87% similarity) with the carboxy-terminus of RNase H from copia (FIG. 17). In all copia/Ty1-like retrotransposons, the RH coding sequence is at the 3′ end of the pol gene and is closely followed by a polypurine tract (PPT) and the 3′ LTR. However, the RH coding region of pol in SIRE-1 is followed by a long ORF in the region corresponding to retroviral env (see below).

The second ORF within this fragment, i.e., ORF2, extends from nt 219 to nt 1958 The predicted translation product suggests that ORF2 encodes a full-length, envelope (env)-like glycoprotein characteristic of animal retroviruses (FIG. 15A and 15B; SEQ ID NOs: 10 and 59 and FIG. 16; SEQ ID NO: 84). Retroviral envelope proteins are synthesized from a spliced transcript in which the initiation codon is supplied by the gag region, which for SIRE-1 was found in the 2.4 kb cDNA clone (Example 1; SEQ ID NO: 3). The amino-terminal one-third of the SIRE-1 env sequence is rich in proline, serine, and threonine codons, with the latter two possibly serving as O-glycosylation sites. There are also a small number of asparagines in this region that might serve as N-glycosylation sites.

Although the predicted amino acid sequence of ORF2 does not exhibit significant amino acid homology with the known env proteins, its predicted secondary structure is typical of animal retrovirus env proteins. Failure to find high amino acid homology with other retroviral proteins is not surprising, as it is likely that SIRE-1 and gol the animal retroviruses diverged before either had acquired an env encoding region.

A typical retroviral env protein has a signal peptide near the amino-terminus. There is a likely hydrophobic signal peptide at codons 22-43 of the SIRE-1 env sequence (FIG. 16; SEQ ID NO: 84). Near the carboxy-terminus of retroviral envelope proteins, a hydrophobic domain serves to anchor the molecules in the membrane such that the protein is oriented with the N-terminus outside the cell and the C-terminus within the cytoplasm. Codons 511 to 531 of the SIRE-1 env sequence (SEQ ID NO: 84) constitute a hydrophobic region that may provide this function (FIG. 16). These assignments and the appropriate membrane orientations are strongly supported by analysis with the transmembrane prediction computer program TMpredict (Hofman and Stofel, 1993) (see below).

ORF2 is 647 codons in length, and the derived, unmodified theoretical protein has a molecular weight of 70 kD. Despite its location immediately downstream of pol, the translated env amino acid sequence does not exhibit significant sequence identity to any reported retroviral env protein. This result is not entirely unexpected because known env sequences constitute a very heterogeneous population, and pair-wise comparisons often fail to demonstrate significant sequence congruence (Doolittle, et al., 1989; McClure, 1991). Alternatively, ORF2 could be a transduced cellular sequence. For example, Bst1 from maize, a low copy-number LTR retrotransposon that lacks its own RT (Johns, et al., 1989; Jin and Bennetzen, 1989), encodes domains derived from a maize plasma membrane H-ATPase (Bureau, et al., 1994; Palmgren, 1994).

Retroviral env genes encode polypeptides that are cleaved by host proteases into surface (SU) and transmembrane (TM) peptides, respectively, which are subsequently rejoined through disulfide linkages (Hunter and Swanstrom, 1990). While the primary sequences of these proteins may be diverse, all retroviral env proteins are glycosylated and share three functionally conserved hydrophobic domains: a signal peptide near the amino terminus of SU, a membrane fusion peptide near the amino terminus of TM, and a distal anchor peptide (Hunter and Swanstrom, 1990).

Retroviral env glycoproteins contain between four and thirty N-glycosylated asparagines at Asn-Xaa-Ser/Thr motifs (Hunter and Swanstrom, 1990), with SU generally more heavily glycosylated than TM. The conceptual translation product of ORF2 from SIRE-1 has only two Asn in this context. However, retroelement env proteins are also known to be O-glycosylated at Ser and Thr residues (Pinter and Honnen, 1988). O-glycosylation is correlated with clusters of hydroxy amino acids with elevated frequencies of Pro (Wilson et al., 1991). The amino half of the theoretical SIRE-1 protein (corresponding to SU) conforms to this pattern, and many of the hydroxy amino acids in the carboxyl half of the protein are adjacent to Pro. The amino acid composition of one extended proline-rich region encompassing amino acids 60 through 127 (SEQ ID NO: 83) is similar to the 60-amino acid proline-rich neutralization (PRN) domain of SU from feline leukemia virus (FeLV) (Fontenot et al., 1994). Pro makes up 18% in both and hydroxy amino acids are 20% in the FeLV PRN and 22% in SIRE-1. Gln is 9% in FeLV and 10% in SIRE-1, and while the PRN of FeLV contains no aromatic amino acids, the comparable SIRE-1 region contains only one. In SIRE-1, the spacing of many of the Pro residues in this region and beyond (Xaa-Pro-Yaa)_(n) or (Xaa-Pro)_(n) is characteristic of many structural membrane proteins from both eukaryotes and prokaryotes (Williamson, 1994).

The putative env protein sequence was evaluated for the presence of hydrophobic, membrane-spanning helices using TMpredict (Hofmann and Stoffel, 1993). The program returned two possible transmembrane regions with high confidence values and a third somewhat below the margin of significance (FIG. 23). The first predicted helix encompasses amino acids 22 to 43 (SEQ ID NO: 83), a typical signal peptide location. The second predicted transmembrane helix extends from amino acid 510 to amino acid 530 (SEQ ID NO: 83), and corresponds to the general location of retroviral anchor peptides. Although of questionable statistical significance, the third predicted transmembrane helix, from amino acids 465 to 485, is in a location that could correspond to that of viral membrane fusion peptides.

Only two retroviral env peptides have been structurally characterized by X-ray crystallography (Chan et al., 1997; Fass et al., 1996), but several env SU and TM sequences have been analyzed by structural prediction computational programs (Hunter and Swanstrom, 1990; Gallaher et al., 1995; Gallaher et al., 1989). Analysis of the ORF2 sequence using the computer program NNpredict (Kneller et al., 1990) suggests the presence of long α-helices and regions of β-sheets (FIG. 20) typically found in env proteins. The evaluation of ORF2 using several other programs (Deleage and Roux, 1987; Georjon and Deleage, 1995; Georjon and Deleage, 1994; Gibrat et al., 1987; Levin et al., 1986), yielded predictions of multiple α-helices similar to those of corresponding regions of other retroviral env proteins (Hunter and Swanstrom, 1990; Gallaher et al., 1995; Gallaher et al., 1989).

ORF2 (SEQ ID NO: 83) was also evaluated for the possible presence of coiled-coils (Lupas et al., 1991). Amino acids 580 to 611 were predicted to form a coiled-coil with very high confidence (FIG. 23). The sequence adheres well to the heptad repeat sequence identified in several virus fusion peptides (Chambers et al., 1990). The predicted coiled-coil in the TM domains of HIV and Moloney murine leukemia virus have recently been confirmed by X-ray crystallography (Chan et al., 1997; Fass et al., 1996).

Retroviral env proteins are generated from spliced transcripts (Varmus and Brown, 1989; Hunter and Swanstrom, 1990). In the case of some avian retroviruses, splicing leads to an in-frame fusion of the gag start codon with the 5′ end of the env coding region (Hunter and Swanstrom, 1990), obviating the need for an initiating AUG in env. An analogous splice in a SIRE-1 transcript would serve the same purpose, although no splice donor or acceptor consensus sequences are present in the expected regions. Cleavage of env proteins into SU and TM generally occurs at a conserved site containing the consensus sequence Arg-Xaa-Lys-Arg (Hunter and Swanstrom, 1990). This sequence does not appear in the putative SIRE-1 env, but there are several similarly basic tetrapeptide candidates for such a cleavage site (FIG. 23). The Lys-Lys-Gly-Lys (SEQ ID NO: 82) at residues 439-442 would generate a TM protein of 22.3 kD with the fusion peptide near the amino terminus. The corresponding SU would be 48.7 kD.

To confirm that the putative env gene was not a library or cloning artifact, and that most, if not all, genomic copies of SIRE-1 were organized in the same way as the clone, SIRE-1 genomic DNA was digested with several restriction enzymes and a Southern blot was probed with sequences from the env and gag subclone regions. The intensity of hybridization of an env probe to genomic DNA (data not shown) was similar to that for the gag probe that had previously been used to establish the moderately high copy number of SIRE-1 (Laten and Morris, 1993). In addition, gag and env probes hybridized to the same 10.5 kb HpaI fragment (data not shown). Although the possibility cannot be ruled out, this env-like ORF is probably not a transduced host gene. The presence of this ORF in most if not all of the several hundred copies of SIRE-1 suggests that this gene is an integral part of the retroelement genome.

Alternate splicing could result in an additional ORF extending from nt 1834 to 2166, thereby encoding a 110-amino acid peptide. Such alternate splicing of retroviral transcripts at similar sites has been shown to lead to the production of trans-acting factors, which may be useful in modulating gene expression in accordance with the present invention.

To identify the LTR, the DNA sequence (SEQ ID NO: 8) from the 4.2 kb XbaI fragment was aligned with that from the SIRE-1 cDNA clone (SEQ ID NO: 3) which contained the last 178 bp of the 5′ LTR. Sequence alignments were made using the Genetics Computer Group package (Devereux et al., 1984). The GCG analysis confirmed that the genomic subclone contained a 3′ LTR and fixed the location of the 3′ end of the LTR at nt 3686 in the sequence AATTTCA (FIG. 3; SEQ ID NO: 8), beyond which the two sequences diverged. Although the region of LTR overlap was virtually identical (98% sequence identity), the moderately high copy number of SIRE-1 makes it unlikely that the cDNA and genomic clones represent copies of the same element.

Upstream of the genomic LTR there are several polypurine regions ranging in length from 11 to 16 nucleotides (FIGS. 13 and 14). Such sites are known to serve as origins for initiation of retroelement plus-strand synthesis. In addition, the SIRE-1 LTR contains appropriately located sequences that strongly resemble consensus sequences for retroviral promoter elements and polyadenylation signals.

The 538 nucleotides of flanking DNA adjacent to the 3′-end of the SIRE-1 sequence (SEQ ID NO: 8) comprises an uninterrupted open reading frame (FIG. 14). This strongly suggests that the SIRE-1 insertion disrupted a functional gene. As the G. max cultivar is essentially a tetraploid, its genome can accommodate some gene disruptions without major phenotypic consequences. The predicted translation product of the flanking DNA is relatively hydrophilic and is rich in asparagine and glutamine codons. No significant homology was found with known plant proteins, however.

To obtain other subclones of SIRE-1, the genomic SIRE-1 λFIXII bacteriophage DNA was double-digested with Hind III (which does not digest λFIXII DNA) and Sac I (which does digest λFIXII DNA in the multicloning region). This digest generated 10 fragments (FIG. 24). The two largest fragments, 20 kb and 9 kb, respectively, are known to constitute the lambda phage arms. The other eight fragments collectively constituted 19 kb of SIRE-1 genomic sequence. Individual digests of the genomic clone with Hind III and Sac I, respectively, revealed that the 2.1 kb and 1-5 kb fragments produced in the double digest were adjacent to the lambda phage arms (data not shown). Therefore, these two fragments each have Hind III and Sac I termini, while the other 6 fragments have only Hind III termini.

Southern blot hybridizations were conducted with the Hind III/Sac I double-digested SIRE-1 DNA using probes derived from the LTR, gag, and env regions of the 4.2 kb Xba I fragment, respectively (FIG. 25). These experiments revealed that the env sequence lies within the 4.1 kb fragment (FIG. 26); the LTR regions are contained within the 4.3 kb and 2.7 kb fragments; and the gag region is also contained within the 4.3 kb fragment (FIG. 27).

The 4.1 kb fragment (containing at least a portion of the env region) and the 4.3 kb fragment (containing at least a portion of the gag region) were each subcloned into pSPORT-1 vectors and the constructs were separately transformed into DH10B E. coli cells. Recombinant plasmids were detected by restriction digestion and Southern hybridization. The vector construct comprising the 4.1 kb fragment was named pEG4.1 (FIG. 28), and the vector construct comprising the 4.3 kb fragment was named pEG4.3 (FIG. 29).

The pEG4.1 construct was sequenced using M13/pUC universal primers (pUC-forward and -reverse; SEQ ID NOS: 12, 14) and SIRE-1 specific primers (FIG. 30; SEQ ID NOS: 39-49) as described above. Translation of the nucleotide sequence obtained thereby (FIGS. 31a-c; SEQ ID NO: 50) revealed a long uninterrupted open reading frame encoding 942 amino acids (FIG. 32; SEQ ID NO: 51). The 3′ terminus of the 4.1 kb Hind III fragment overlapped the 5′ terminus of the 4.2 kb Xba I fragment (described above, containing the env region) by approximately 1.5 kb. Translation of the remaining 2.6 kb sequence revealed regions exhibiting strong homologies to the integrase, reverse transcriptase, and RNase H regions of known retrotransposons.

The 4.3 kb Hind III fragment contained in pEG4.3 was partially sequenced using pUC universal primers (REF; SEQ ID NOS: 12,14). The 5′ terminal region of the 4.3 kb fragment was found to contain sequence identical to that of the putative 3′ LTR contained within the 3′ terminal region of the 4.2 kb Xba I (env-containing) fragment (SEQ ID NO: 8). The 3′ terminal region of the 4.3 kb Xba I fragment contained sequences exhibiting strong homology to the amino-terminal region of the integrase (int) domain of known retrotransposons.

A region encompassing 400 amino acid residues predicted from the contiguous nucleotide sequences of the 3′-terminal region of the 4.3 kb fragment and the 5′-terminal region of the 4.1 kb fragment, respectively, appears to constitute an integrase (int) domain (SEQ ID NO: 52). The predicted amino acid sequence of this putative int domain was compared against the BLAST-P peptide database. Significant homology was found with copia-like retrotransposons, with the strongest homology being to the Opie-2 element from maize, which exhibited 39.8% identity and 58.5% similarity at the amino acid level, with three sequence gaps (FIG. 33). The putative SIRE-1 and Opie-2 elements each contain a conserved HHCC (H-X4-H, C-X2-C) motif, which is usually found at the amino-terminus of retrotransposon integrase domains (FIG. 33). The SIRE-1 and Opie-2 elements also each contain a D(10)D(35)E motif (i.e., two aspartate residues within 10 residues of each other, and a glutamate residue within 35 residues of the pair in the carboxy-terminal direction) (FIG. 33).

The break point between the integrase (int) and the reverse transcriptase (RT) domains of SIRE-1 was determined by comparison of the 4.1 kb fragment sequence with the sequences of retroelements where the break point has been determined experimentally (Doolittle et al., 1989; McClure, 1991; Springer and Britten, 1993; Taylor et al., 1994; Rogers et al., 1995). The predicted amino acid sequence (SEQ ID NO: 53) of the reverse transcriptase domain extends from residue 401 to residue 781. This predicted sequence was compared against the BLAST-P peptide sequence database. Significant homology was found between the putative SIRE-1 RT region and the RT regions of copia-like retrotransposons (FIG. 34). Again, the most significant match was to Opie-2 from maize, which exhibited 560 identity and 71. similarity at the amino acid level, with one sequence gap (FIG. 34). Several regions in which the SIRE-1 RT exhibits near identity to that of Opie-2 encompass sequences that have proved useful in studying the phylogenetic relationships of retroelements (Xiong and Eickbush, 1990).

The break point between the reverse transcriptase (RT) and Ribonuclease H (RH) regions of the SIRE-1 4.1 kb fragment sequence was also predicted by comparison against those of known retroelements. The RH domain of SIRE-1 appears to encompass the predicted amino acids 782 to 942. This predicted sequence (SEQ ID NO: 54) was compared against the BLAST-P peptide sequence database. Not surprisingly, the strongest homology was found with the RH element of maize Opie-2, which exhibited 53.1% identity and 71.0% similarity to the predicted SIRE-1 RH region (FIG. 35). The SIRE-1 RH domain also contains the DEDD motif found in the RH elements of most known retrotransposons (FIG. 35).

These data confirm that SIRE-1 is a retroviral family whose genomic structure is based on a copia/Ty1-like organization. The genomic organization of all animal retroviruses (from vertebrates and Drosophila) is patterned after gypsy/Ty3-like retrotransposons. Neither retroviral genomes nor virions have been reported in plants, although both classes of retrotransposons are widespread. In plants, virus spread is mediated by intercellular movement (Mushegian and Koonin, 1993). However, very few plant virus genomes encode an env gene. Those that do—rhabdoviruses and bunyaviruses (Matthews, 1991)—also infect animal hosts where env proteins mediate viral-host cell membrane fusion. Plant cell walls may preclude this mode of virus transfer, and whether the env proteins of these viruses serve any function in their plant hosts is not known. Thus, the presence of an env gene in SIRE-1 suggests that SIRE-1 may have originally been an infectious invertebrate retrovirus.

The overall restriction site homogeneity, the presence of long, uninterrupted ORFs within and adjacent to SIRE-1, and the near identity of the 5′ and 3′ SIRE-1 LTRs suggest that SIRE-1 is not an evolutionary relic, and may be modified to function as an infectious retrovirus and/or intracellular retrotransposon.

The genomic clone may be used as a SIRE-1 genomic probe. The probe may be hybridized to Southern blots of complete and partial digests of soybean DNA to generate a consensus restriction map (Sambrook et al., 1989). Additionally, restriction maps of additional clones and the genomic DNA consensus may be compared to more fully assess SIRE-1 heterogeneity. The polymorphic sequences of clone populations may then be used to determine expression-related features and phylogenetic relationships to other plant and animal elements.

The env, gag, and pol nucleotide sequences may be used to generate oligonucleotide or cDNA probes to detect transcription of these regions (Navot et al., 1989), and antibodies generated against SIRE-1 proteins may be used to detect the presence of retroviral protein expression in various plant tissues (Hsu and Lawson, 1991). Moreover, reverse transcriptase (RT) and integrase (int) probes may be created by restriction digestion or PCR and used to assess the functional significance of the unprecedented length of SIRE-1.

EXAMPLE 3 Northern Hybridization Analysis of SIRE-1 Transcriptional Activity

The use of the SIRE-1 polynucleotide as a tool for genetic engineering may require the expression of sequences therefrom. It may therefore be desirable to determine growing conditions under which plants or plant cell cultures that have been infected or transduced with SIRE-1-derived DNA exhibit elevated or depressed transcriptional activity. There are many examples in which the transcriptional activity of a virus is enhanced during periods in which its host experiences environmental stress. Therefore, experiments may be conducted to determine growth conditions (or conditions of stress) optimal for the regulation of SIRE-1 expression.

The presence of SIRE-1-specific transcripts in plants such as soybean may be evaluated by Northern hybridization (Sambrook et al., 1989). For example several G. max cultivars, including the Asgrow Mutable line, an unstable soybean isolate (Groose & Palmer, 1987; Groose et at, 1983), and Glycine soja strains (from a range of origins) may be grown from seed obtained from the U.S. Regional Soybean Laboratory in Urbana, Ill.

Plants may be grown under optimal and adverse (stress) conditions in growth chambers or in a greenhouse, and the transcriptional activity of SIRE-1 in plants subjected to adverse conditions may then be compared to that in plants grown in normal conditions.

Many potential adverse growing conditions are well-known in the art. For example, seedlings may be grown in vermiculite and subjected to temperatures ranging from 15° C. to 40° C. Plants may also be subjected to salt stress by applying NaCl solutions ranging up to 20%, or to osmotic stress by adding solutions containing PEG 8000. Plants growing under each or several of these conditions may be harvested at various times to assess the temporal relationship of the adverse condition to the transcriptional activity of SIRE-1. To assess the impact of viral infection, leaf tissue may be inoculated with a virus such as soybean mosaic virus and harvested at 2, 5, 10 and 20 days after infection (Mansky et al., 1991).

In addition, the transcriptional activity of SIRE-1 may be assessed in plant tissue cultures. Tissue cultures may be initiated from roots, cotyledons, or leaves from selected cultivars as described (Amberger et al, 1992; Roth et al., 1989; Shoemaker et al., 1991). Tissue can then be transferred to Petri plates containing Gamborg's B5 medium supplemented with kinetin, casein hydrolysate and concentrations of 2,4-D ranging from 1 to 20 μM. After the formation of callus, suspension cultures may be initiated and maintained in liquid medium (Roth et al., 1989). These cultures may then be exposed to adverse growing conditions as described above.

Total RNA may be isolated from seeds, cotyledons, leaves, roots, shoot tips, or cultured cells using commercial kits such as RNeasy™ (Qiagen, Chatsworth, Calif.). If necessary, polyadenylated RNA may be isolated from total RNA using the PolyATtrac™ mRNA isolation system (Promega, Madison, Wis.). Isolated RNA may then be applied to nylon membranes (Gene Screen Plus™, New England Nuclear, Boston, Mass.) using a slot-blot apparatus, denatured, and probed with end-labeled oligomers or radiolabeled cDNAs corresponding to the gag or pol regions of SIRE-1 (Sambrook et al., 1989). RNA samples that give positive signals may be fractionated on 1% agarose-formaldehyde gels, blotted to nylon membranes, and probed as above. Preliminary studies of SIRE-1 RNA transcripts in G. max (using the slot-blot procedures described above) have revealed the presence of high levels of gag transcripts in leaf tissues.

As retro-elements commonly produce polyprotein-encoding transcripts that traverse nearly the entire element, functional SIRE-1 transcripts could exceed 10 kb in length. This could limit the applicability of agarose-formaldehyde gel separations. Alternatively, isolated RNA can be analyzed for the presence of SIRE-1 transcripts by ribonuclease (RNase) protection assays well-known in the art. For example, RNA isolated from plants grown in the above-described conditions can be hybridized to SIRE-1-derived radiolabeled RNA probe in solution and then exposed to one or more of several available RNases. The double-stranded hybrid formed by the probe and target RNA is protected from RNase digestion. The protected RNA can be fractionated on a denaturing polyacrylamide gel, blotted to a nylon membrane, and visualized by autoradiography.

EXAMPLE 4 Detection of Retroelement Proteins by Western Hybridization Analysis

Plant tissue samples that contain SIRE-1-specific transcripts may be analyzed for the presence of SIRE-1-specific proteins or for proteins expressed by heterologous genes inserted into a SIRE-1 derived vector. Protein recovered from these tissues may be spotted on nylon membranes and assayed for the presence of nucleocapsid, protease, and RT polypeptides by Western hybridization (Sambrook et al., 1989).

Polyclonal antisera against SIRE-1 proteins (or fusion constructs containing SIRE-1 and heterologous peptide sequences) to be detected in these hybridizations can be obtained using methods well-known in the art. For example, oligopeptides may be designed and synthesized using sequence information from the cDNA and genomic clones. The synthetic oligopeptides may be coupled to carrier protein using for example gluteraldehyde, and antibodies against these raised in rabbits and affinity-purified as is well-known in the art (Harlow and Lane, 1988).

Alternatively, polyclonal antisera may be raised against fusion proteins produced by inserting the appropriate SIRE-1 DNA fragments (or DNA encoding the heterologous proteins) in a protein expression vector like pPROEX-1 (Life Technologies, Gaithersburg, Md.) and isolating the fusion protein according to the manufacturer's instructions.

Monoclonal antibody preparations against SIRE-1 proteins or fusion proteins may also be isolated from hybridoma cells derived from splenocytes or thymocytes of mice immunized with such proteins according to methods well-known in the art (Harlow and Lane, 1988).

EXAMPLE 5 In vitro Transcription and Translation of SIRE-1 Transcripts

It may be desirable to produce SIRE-1 polypeptides in vitro for use in producing antibodies or for capsid reconstitution studies and to provide reagents for in vitro packaging of retroviral polynucleotides. Production of SIRE-1 polypeptides in a cell-free environment may be accomplished by creating cDNAs from SIRE-1 mRNA transcripts, inserting those cDNAs into plasmids, propagating the plasmids, and utilizing such plasmids in in vitro transcription/translation reactions as are well-known in the art. cDNAs may be recovered from full-length SIRE-1 transcripts isolated from soybean total or poly-A-selected RNA. Such cDNAs may be produced using reagents and reactions optimized for long transcripts (Nathan et al., 1995). Total or poly-A-selected soybean RNA may be reverse-transcribed with SuperScript II™ reverse transcriptase (Life Technologies, Gaithersburg, Md.) using an oligo(dT) primer. RNase H may be added and the single-stranded cDNA amplified using LA Tag DNA polymerase (Oncor) with oligo(dT) and 5′ primers derived from the proximal end of the SIRE-1 gag and/or env cDNA sequences. The 5′ end of each PCR primer may contain a restriction enzyme recognition sequence for subsequent vector ligation in the appropriate orientation and sequences that would facilitate enhanced transcription and/or translation.

Amplified cDNAs may be initially characterized by agarose gel electrophoresis and Southern hybridization using gag-, pol- and env-specific cDNA or oligonucleotide probes. The amplified DNAs may be ligated into pSPORT-1 (Life Technologies, Gaithersburg, Md.), a vector designed to carry large inserts, and the recombinant plasmids used to transform competent E. coli DH5α cells (Life Technologies, Gaithersburg, Md.). Plasmid DNA may be recovered from transformants and evaluated by restriction mapping and Southern hybridization as described above. Selected regions of several cDNAs may be sequenced with primers based on the sequence obtained from the genomic SIRE-1 clone. cDNA variability may be assessed and quantitatively compared to that observed with Tntl transcripts in tobacco, which constitute a quasispecies-like collection (Casacuberta et al., 1995). The transcriptional initiation site(s) may be evaluated by primer extension and/or S1 nuclease digestion (Sambrook et al., 1989).

Alternatively, a parallel series of experiments may be run to generate translatable mRNAs. SIRE-1-specific cDNAs may be generated as above, except that the 5′ PCR primer may be derived from the beginning of the gag and pol coding regions. The cDNA sequence suggests that a single gag-pol ORF may not be present in SIRE-1, and translation of the downstream pol region requires readthrough of a stop codon and/or a frameshift. It is probable that the ribosomes in the in vitro translation system may not emulate the in vivo translation. For expression of the pol region, the cDNAs may be amplified using a 5′ primer derived from the proximal end of the pol ORF.

Plasmid DNAs containing SIRE-1 cDNAs may be recovered, and coupled in vitro transcription-translation assays may be run (Switzer and Heneine, 1995) using a reticulocyte lysate system (Promega, Madison, Wis.). Translation products may be analyzed by SDS-PAGE and Western hybridization as described above.

As an alternative to coupled in vitro transcription and translation, SIRE-1 cDNAs may be cloned into the protein expression vector pPROEX-1 (Life Technologies, Gaithersburg, Md.), and fusion proteins, expressed in E. coli and recovered as described by the manufacturer. SIRE-1 cDNAs utilized in the above-mentioned reactions could include those encoding analogs, homologs, or fragments of the full-length SIRE-1 gag, pol, or env proteins. These proteins, although not identical to proteins encoded by the SIRE-1 polynucleotides disclosed herein, may nevertheless be useful if they retain at least one biological property of SIRE-1 proteins. Such proteins may be used for antibody generation as described above, or for subsequent protein conformation studies.

EXAMPLE 6 Modification of SIRE-1 for Use in Non-Replicative Transduction of Plant Cells

SIRE-1 may be adopted for use as a retroviral vector in legumes, e.g., soybean, common beans, and alfalfa, cereals, e.g., rice, wheat, and barley, and other agronomically important crops such as fruit trees, conifers, and hardwoods. The use of a plant retrovirus for introduction of DNA sequences into plant cells presents several advantages over previously-known methods. First, unlike other plant viral vectors (Joshi and Joshi, 1991; Potrykus, 1991), the SIRE-1 pro-retrovirus may integrate into the host genome and generate stable transformants (Crystal, 1995; Miller, 1992; Smith, 1995).

Second, although other vectors have been used to introduce nucleic acid into plant genomes, they have serious limitations. For example, Ti plasmid-based vectors lead to integrative transformation, but their bacterial host, Agrobacterium tumefaciens, has a limited host range that does not include many legumes or most cereals (Christou, 1995; Potrykus, 1991).

Finally, physical transformation methods (i.e., biolistic projection or microinjection) are far less efficient than viral infection in introducing DNA constructs into desired cells. These physical methods also generally require regeneration of adult plants by somatic embryogenesis (Christou, 1995; Potrykus, 1991).

A full-length SIRE-1 pro-retroviral DNA and vectors derived therefrom will be competent to effect transduction into plant host cells and integration into the host genome, using any of the foregoing methods. However, it may be desirable to modify SIRE-1 vectors so as to limit the region of integration, to restrict subsequent transposition events, to add DNA sequences to promote homologous recombination between a vector and a target region of the genome, and to insure against infectious spread of a potentially pathogenic agent.

SIRE-1 may be modified in a manner analogous to that used for vertebrate retroviruses to create recombinant viral vectors that may infect host cells but not complete an infection cycle. For vertebrate retroviral vectors, this is accomplished by deleting or disabling the trans-acting elements (i.e., gag, pol, and env) from the vector to be transduced into the host cell, while leaving intact the cis-acting elements (i.e., LTRs and packaging signals). This is followed by transduction of the modified vector into retrovirus packaging cell lines or tissue cultures (Miller, 1992; Smith, 1995) that may contribute the necessary trans-acting elements.

Thus, the present invention contemplates SIRE-1 constructs in which sequences encoding the trans-acting factors (e.g., gag, pol, and env), the LTRs, or the packaging signals have been mutated or deleted, either singly or in combination. Mutations may be easily accomplished using PCR-mediated site-directed or cassette mutagenesis techniques as are well-known in the art.

The trans-factor encoding sequences may be deleted by digestion of the SIRE-1 viral DNA with appropriate restriction enzymes. Those of ordinary skill in the art will be readily able to determine the appropriate restriction enzyme recognition sites in the SIRE-1 DNA that will allow for removal of the appropriate trans-factor DNA segments while leaving intact essential cis element sequences. One approach would be to digest the SIRE-1 DNA with a restriction enzyme that would cleave at sites located at or near the 5′ and 3′ boundaries of the ORF2 region (FIG. 14) such that all or part of the env-encoding region could be-removed from the vector.

Restriction digestion may be followed by recovery and purification of the digested vector DNA fragments containing cis factor sequences, followed by religation of the digested termini (Sambrook et al. 1989). Alternatively, appropriate double-stranded DNA linkers may be ligated to the digested ends of the vector DNA in order to maintain or create a proper reading frame. As another possibility, linker sequences containing one or more endonuclease restriction enzyme recognition sites may be ligated to the ends of the digested vector DNA, and these ends then religated in order to facilitate subsequent insertion of heterologous gene sequences.

Infection of packaging cells or tissue cultures with the modified SIRE-1 vector may allow for the recovery and use of a non-replicative recombinant vector in a functional virion particle that may be capable of intercellular transport (for example, through plasmodesmata), host cell penetration, nuclear targeting, and chromosomal integration, but incapable of further transposition. Reporter genes like GUS (β-glucuronidase, Jefferson et al., 1981) or Npt-II (Neomycin phosphoryltransferase, Pridmore, 1987) and others (Croy, 1994) may also be incorporated into SIRE-1 or vectors derived therefrom to allow detection of integration events.

EXAMPLE 7 Production of Plant Retroviral Packaging Cells

Modification of pro-retroviruses for use as vectors is fairly straightforward. In essence, retroviral vectors are simple, containing the 5′ and 3′ LTRs, a packaging sequence, and a transcription unit composed of the recombinant gene or genes of interest and appropriate regulatory elements which include LTRs but which may also include heterologous regulatory elements. To grow the vector, however, the missing trans-factors must be provided using a so-called packaging cell line. Such a cell is engineered to contain integrated copies of gag, pot, and env, but to lack a packaging signal so that no “helper virus” sequences become encapsidated. Additional features may be added to or removed from the vector and packaging cell line to render the vectors more efficacious or to reduce the possibility of contamination by “helper virus.”

A packaging cell line is produced by means of transfection of a helper virus plasmid encoding gag, pol, and env and by selecting for cells that express the proteins and that can support vector production (Miller, 1990). To avoid replication of helper sequences, one may make deletions in, for example, the packaging signal regions. To avoid recombination between the packaging vector and the replicating vector, the 3′ LTR is commonly deleted and replaced with a polyadenylation sequence (Dougherty et al., 1989). Deletions may also be incorporated into the 5′ LTR to reduce its ability to replicate, and a heterologous promoter may be inserted downstream to maintain expression of the trans-factors (Miller, 1989). Finally, the viral genome may be split into two transcription units, one encoding gag and pol and a second encoding env (Markowitz, 1988). The cis-acting factors may be deleted or modified from these vectors in order to prevent production of replication-competent retrovirus by the packaging cells.

The trans-acting factors encoded by the helper virus construct may include the native factors from SIRE-1, modified SIRE-1 factors, or other proretrovirus-derived factors that may result in an increased or alternative host range or higher efficiency of viral production or transduction efficiency (Smith, 1995). Thus, the present invention encompasses vectors containing sequences encoding the trans-acting factors from SIRE-1, either singly or in various combination, for use in creating packaging cells, and the packaging cells themselves.

To manipulate target cell specificity, the env gene of the helper virus/packaging cell line may be varied. A successful approach has been to remove sequences from the env gene and replace them with sequences encoding proteins with a different specificity (Russell et al., 1993). For example, erythropoietin sequences have been incorporated into mammalian retroviruses to target the EPO receptor (Kassahara et al., 1994). Another approach has been to incorporate a single-chain antibody into the env sequence (Chu et al., 1994). Finally, the ability of retroviruses to incorporate glycoproteins from other viruses into their envelope has been utilized to produce so-called pseudotypes (Dong et al., 1992). The pseudotype retrovirus acquires the infective range of the glycoprotein donor, and usually is more stable as well. Analogous strategies may be used in SIRE-1 retroviral vectors to manipulate the host range beyond soybean by inserting into the SIRE-1 env gene ligand-, receptor-, or single-chain antibody-encoding fragments that could recognize, or be recognized by, proteins from other plant species, such as rice or maize.

EXAMPLE 8 Transduction of the SIRE-1 Plant Proretrovirus into Plant Cells

If the SIRE-1 proretrovirus or vectors derived therefrom integrate into the genome of a cell transduced with such DNA, all cells derived from the original cell transfected with the SIRE-1 vector may contain the retroviral insertion. Infections are commonly targeted to embryonic, meristematic, or germ line cells to enable transmission to progeny plants. Since certain plants (such as G. max) are self-fertilizing, transfection of embryos or meristematic tissue may lead to homozygosity of inserted DNA in some F₁ offspring, although the proportion of seed homozygous for a particular insertion event may need to be empirically tested. Dominant changes may be manifested in heterozygous progeny. Transfection of various adult tissues, especially meristems and ovaries, or seeds, pollen, protoplasts, or callus, may be performed by standard inoculation and/or co-incubation techniques which are well known (Potrykus, 1991). Viruses may also be inoculated into phloem for transport to distant sites. In some cases, physical methods such as biolistic projection, microinjection, or macroinjection may be necessary or preferred to transduce SIRE-1 into plant cells or tissues (Draper and Scott, 1991; Potrykus, 1991).

EXAMPLE 9 Use of SIRE-1 as a Gene Transfer Vector

SIRE-1 may be modified to carry useful gene sequences (e.g., gene sequences encoding useful proteins) or, alternatively, genes to produce antisense transcripts against undesirable endogenous sequences or to introduce into the genome gene regulatory elements which may regulate transcription of an adjacent gene. This may be easily accomplished by restriction enzyme digestion of the vector DNA at sites near the 5′ and 3′ boundaries of the ORFs encoding the gag, pot, and/or env proteins (as described above), isolating the remaining vector DNA, and either ligating a heterologous DNA fragment between the digested vector termini or alternatively by recombinantly inserting a multicloning site (Sambrook, et al., 1989) between the digested vector termini to allow for subsequent facile restriction enzyme digestion and recombination of digested vector and heterologous DNAs. Heterologous gene sequences may be operably linked to (heterologous) host-cell specific promoter sequences (Waugh and Brown 1991), or their transcription may be driven by the SIRE-1 LTR promotor activity. The heterologous gene sequences may encode any of a variety of polypeptides whose expression may result in useful phenotypic changes of the host cell and plant. By way of example, introduction and expression of these heterologous gene sequences in plants may result in the generation of the following exemplary phenotypic variations:

A. Disease Resistance

Many agronomically important crops are susceptible to a variety of diseases, viral infections, and bacterial or fungal infestations. Resistance to these conditions results in higher crop yields and decreased use of bacteriocidal and fungicidal compositions. Transfer of genes conferring resistance to diseases and/or viral or bacterial infection is an object of the present invention.

Many plant genomes, including soybean, are currently being mapped (Keim et al. 1996). In addition, genetic loci associated with disease resistance have been identified in many plant lines. For example, resistance markers and quantitative trait loci (QTL) for many soybean diseases have been linked to restriction fragment length polymorphism (RFLP), RAPD (Randomly Amplified Polymorphic DNA), and STS (Sequence Tag Sites) genome markers. These include bacterial blight, downy mildew (Bernard and Cremeens, 1971), phytophthora root rot (Diers et al. 1992), powdery mildew (Lohnes and Bernard, 1992), soybean rootknot nematode infection (Luzzi et al. 1994), phomopsis seed decay, cyst nematode infection (Baltazar and Mansur 1992; Boutin et al. 1992; Rao-Arelli et al. 1992; Young 1996), soybean mosaic virus (Chen et al. 1993), soybean rust (Hartwig and Bromfield 1983), stem canker (Bowers et al. 1993; Kilen and Hartwig 1987), sudden death syndrome (Prabhu et al. 1996), purple seed stain and leaf blight, and brown spot disease.

Both YAC (yeast artificial chromosome) and BAC (bacterial artificial chromosome) soybean libraries have been constructed (Funk and Colchinsky, 1994), and resistance markers have been assigned to particular clones in these libraries. The availability of these gene sequences will allow for insertion of DNA fragments Ire encoding such genes into SIRE-1 proretrovirus-derived vectors of the present invention using standard recombinant techniques as have been described above (Sambrook et al., 1989). The recombinant vector may then be transduced into target plant cells, where the resistance gene may be expressed episomally or following integration of the vector into the host plant genome.

Transfer of resistance to viral infection to target plant cells is an important object of the present invention. The expression of a viral coat protein in a plant has been shown to diminish the ability of the virus to subsequently infect the plant and spread systemically; thus viral resistance may be mediated by vector-sponsored transfer of viral gene sequences into susceptible plant hosts (Beachy, 1990; Fitchen and Beachy, 1993). Many different viral coat protein genes have been introduced into plant genomes, expressed, and found to confer viral tolerance, including tobacco mosaic virus, cucumber mosaic virus, alfalfa mosaic virus, tobacco streak virus, tobacco rattle virus, potato viruses X and Y, and tobacco etch virus (Beachy, 1990; Gasser and Fraley, 1989; Golemboski et al., 1990; Hemenway et al., 1988; Hill et al., 1991). This approach to viral resistance is especially promising, as the introduction of a viral coat protein from one virus using the vectors of the present invention may often confer tolerance to a range of seemingly unrelated viruses (Beachy, 1990). Moreover, transgenic plants expressing viral coat proteins exhibit viral tolerance in the field as well as in a laboratory setting (Nelson et al., 1988).

Plants may also be transformed with a retroviral vector encoding an antisense RNA complementary to a plant virus polynucleotide. Expression of antisense RNA against viral sequences may provide tolerance against the virus by interfering with either the translation of viral mRNAs or the replication of the viral genome. Expression of antisense RNA has been found to confer viral resistance in, among others, potato, tobacco, and cucumber plants (Beachy, 1990; Day et al., 1991; Hemenway et al., 1988; Rezaian et al., 1988).

Using the present invention, DNA fragments encoding viral coat proteins or antisense RNA complementary to viral RNA transcripts may be recombinantly inserted into the SIRE-1 proretrovirus, transduced into susceptible plants, and expressed to confer resistance to a virus.

B. Herbicide Tolerance

The use of herbicides is limited in part by their toxicity to crop species and by the development of resistance in “weed” species (Hathaway, 1989). Increasing tolerance to herbicides may increase yield and augment the spectrum of herbicides available for use to curtail weed growth. A wider range of suitable herbicides may also retard the development of resistance in weed species (LeBaron and McFarland, 1990), thereby decreasing the overall need for herbicides. Herbicide classes include, for example, acetanilides (e.g., alachlor), aliphatics (e.g., glyphosphate), dinitroanilines (e.g., trifluralin), diphenyl esters (e.g., acifluorfen), imidazolinones (e.g., imazapyr), sulfonylureas (e.g., chlorsulfuron), and triazines (e.g., atrazine).

Two general approaches may be taken in engineering herbicide tolerance: one may alter the level or sensitivity of the target enzyme for the herbicide (such as by altering the enzyme itself, or by decreasing the level or activity of a herbicide transporter), or incorporate or increase the activity of a gene that will detoxify the herbicide (Hathaway, 1989; Stalker, 1991).

An example of the first approach is the introduction (using the vectors and viruses of the present invention) into various crops of genetic constructs leading to overexpression of the enzyme EPSPS (5-enolpyruvylshikimate-3-phosphate synthase), or isoenzymes thereof exhibiting increased tolerance, which confers resistance to the active ingredient in the widely-used herbicide Roundup™, glyphosphate (Shah et al., 1986). The gene for EPSPS was isolated from glyphosphate-resistant E. coli, given a plant promoter, and introduced into plants, where it conferred resistance to the herbicide. Transgenic species carrying resistance to glyphosphate have been developed in tobacco, petunia, tomato, potato, cotton, and Arabidopsis (della-Cioppa et al., 1987; Gasser and Fraley, 1989; Shah et al., 1986).

Similarly, resistance to sulfonylurea compounds, the active ingredients in Glean™ and Oust™ herbicides, has been produced by the introduction of site-specific mutant forms of the gene encoding acetolactate synthase (ALS) into plants (Haughn et al., 1988). Resistance to sulfonylureas has been transferred using this method to tobacco, Brassica, and Arabidopsis (Miki et al., 1990).

Bromoxynil is a herbicide that acts by inhibiting photosystem II. Rather than attempting to modify the target plant gene, resistance to bromoxynil has been conferred by the introduction of a gene encoding a bacterial nitrylase, which can inactivate the compound before it contacts the target enzyme. This strategy has been used to confer bromoxynil resistance to tobacco plants (Stalker et al., 1988).

Genes encoding wild-type or mutant forms of endogenous plant enzymes targeted by herbicide compounds, or enzymes that inactivate herbicide compounds, may be recombinantly inserted into SIRE-1 or vectors derived therefrom and transduced into plant cells. The genes may then be expressed under the control of plant- or tissue-specific promoters (Perlak et al., 1991) to confer herbicide resistance to the transformed plant. The overexpression of normal or mutant forms of enzymes normally present in the wild-type progenitor plant is preferred, as this may decrease the probability of deleterious effects on crop performance or product quality.

C. Insect Resistance

Transduction of functional genes encoding insecticidal products into plants may lead to crop strains that are intrinsically tolerant of insect predators. Such plants would not have to be treated with expensive and ecologically hazardous chemical pesticides. In addition, such insecticides would be effective at much lower concentrations than exogenously applied synthetic pesticides, and because biological insecticides are very specific, they are generally not hazardous to the food consumers.

Insect resistance in plants is generally provided by toxins or repellents (Gatehouse et al., 1991). Using the present invention, insecticidal protoxin genes derived from, for example, several subspecies of Bacillus thuringiensis (Vaeck et al., 1987), may be transduced into plant cells and constitutively expressed therein. This protoxin does not persist in the environment and is non-hazardous to mammals, making it a safe means for protecting plants. The gene for the toxin has been introduced and selectively expressed in a number of plant species including tomato, tobacco, potato, and cotton (Gasser and Fraley, 1989; Brunke and Meussen, 1991).

The trypsin inhibitor protein from cowpea is also an effective insecticide against a variety of insects: its presence restricts the ability of insects to digest food by interfering with hydrolysis of plant proteins (Hilder et al., 1987). As the trypsin inhibitor is a natural plant protein, it may be expressed in plants without adversely affecting the physiology of the host. There are several potential drawbacks to the use of the cowpea trypsin inhibitor, however. Relative to the B. thuringiensis toxin, higher concentrations of inhibitor are required for insecticidal effectiveness (Brunke et al., 1991). Thus, production of the inhibitor may require a more powerful transcriptional promoter (Perlak et al., 1991), and may be more energetically costly for the host plant. In addition, the inhibitor is active in mammalian digestive systems unless inactivated prior to consumption. Inactivation may be accomplished by heating, however, so this may not be a significant drawback to the use of the inhibitor in most crop plants. Moreover, in most crops, the expression of the inhibitor may be restricted to those plant tissues such as leaves or roots that are most exposed to insect predators but are not consumed by mammals through the use of tissue-specific promoter sequences operably linked to the inhibitor gene (Perlak et al., 1991).

These exemplary genes conferring insect resistance or repellence may be inserted into SIRE-1 proretrovirus derived vectors using recombinant methods well-known in the art. These recombinant vectors may then be transduced into soybean and other plants. As more insect resistance and repellence genes are identified, these may be recombinantly inserted into the SIRE-1-derived gene transfer vector and expressed in host plants.

D. Enhanced Nitrogen Fixation and/or Nodulation

Genes whose expression contributes to greater nitrogen fixation and nodulation (Gresshoff and Landau-Ellis, 1994; Qian et al. 1996) may be overexpressed in plant cells by transduction of a recombinant SIRE-1 vector containing DNA fragments from which those genes may be expressed. Alternatively, expression of those genes whose expression leads to reduced nitrogen fixation or nodulation (Wu et al. 1995) may be modulated by the SIRE-1-mediated expression of recombinantly inserted DNA fragments encoding antisense transcripts. Manipulation of these genes may lessen or obviate the current great need for nitrogen-based fertilizers.

E. Enhanced Vigor and/or Growth

Genes from wild progenitor species or non-related species whose expression results in economically valuable growth traits often found in wild progenitor species or non-related species have been discovered (Allen, 1994; Takahashi and Asanuma, 1996). Such genes or gene fragments may be placed under the control of heterologous or native promoters to create a gene cassette, and such cassettes may be recombinantly inserted into SIRE-1 or vectors derived therefrom. These recombinant vectors may then be transduced into plant cells, where expression of the proteins encoded by such genes may lead to the development of plant phenotypes exhibiting economically valuable growth characteristics.

F. Altered Seed Oil/Carbohydrate/Protein Production

Markers have been identified for several genes associated with soybean seed protein and oil content (Lee et al. 1996; Moreira et al. 1996). Transduction and expression of these genes within plants may result in greater seed oil production with lowered linolenic acid content, enhanced seed storage protein production, diminished raffinose-derived oligosaccharide levels, decreased lipoxygenase levels, or decreased protease inhibitor content (which may decrease the nutritive value of some plant proteins in animal feed due to decreased hydrolysis in the digestive tracts of animals). Such genes may be recombinantly inserted into SIRE-1 proretrovirus or vectors derived therefrom, and the recombinant virus or vector may then be used to introduce such genes into plants or plant cells where they may be expressed and may influence the plant phenotype.

The potential food value of certain grains may be improved by altering the amino acid composition of the seed storage proteins. This may be accomplished in at least two ways. First, genes encoding heterologous seed storage proteins composed of a more desirable amino acid mix may be transferred into plants using the vectors and methods of the present invention with an undesirable seed storage protein amino acid composition. This approach has been utilized in several model studies: an oleosin gene from maize was successfully transferred and expressed in Brassica (Lee et al., 1991), and a phaseolin gene from a legume was expressed, and the seed storage protein was appropriately compartmentalized, in tobacco plants (Altenbach et al., 1989).

Second, genes encoding endogenous seed storage proteins may be mutated to contain a more desirable amino acid composition and reintroduced into the host plant using the vectors of the present invention (Hoffman et al., 1988). The effect of these amino acid substitutions on protein conformation and compartmentalization may be lessened by targeting the substitutions to the hypervariable regions near the carboxy-terminus of most seed storage proteins (Dickinson et al., 1990). Genes encoding proteins with altered amino acid compositions may be incorporated into the SIRE-1 retroviral or vectors derived therefrom, and the recombinant virus or vector may then be used to introduce the genes into plant cells in order to introduce changes in protein amino acid composition.

G. Heterologous Protein Production

The present invention contemplates recombinant SIRE-1 virus or vectors derived therefrom that may be used to introduce genes encoding technical enzymes, heterologous storage proteins, or novel polymer-producing enzymes, thus allowing crops to become a novel source for these products.

EXAMPLE 10 Use of SIRE-1 to Induce and Tag Mutations in a Plant Genome

An important object of this invention is the use of the SIRE-1 proretrovirus to establish new landmarks in plant genomes, and to induce and trace new mutations. SIRE-1 may be used to link mutagenesis and element expression. Somaclonal variation has been demonstrated for soybean (Amberger et al., 19921—Freytag et al., 1989; Graybosch et al., 1987; Roth et al., 1989), for example, but little is known about the agents that induce the heritable changes. Persons of ordinary skill in the art will be able to identify new SIRE-1 insertion sites in plant genomes and to correlate these new sites with variant phenotypes. Homozygosity at insertion sites may theoretically be achieved in the F₁ progeny, while dominant insertions may be differentiated from pre-existing integration events if the active element possesses a reporter gene like GUS or Npt. Phenotypes may then be correlated with the newly tagged genomic sites, and sequences flanking the sites may be easily cloned and sequenced (Sambrook, et al., 1989).

SIRE-1 may also be used to investigate the relationship between “genomic stress” and transposable element activity by seeking clues in the LTR regions to the identity of host proteins that might regulate element expression. The presence and expression of these proteins may then be correlated with the adverse conditions known to induce element expression.

The availability of a functional proretrovirus in a major plant group has far-ranging applications to applied genetic manipulations and to basic biological problems concerning gene function, genome organization, and evolution. A better understanding of these issues may be valuable in identifying and mapping important new loci. Understanding the relationships between plant health and element mobilization may provide invaluable insights into short- and long-term consequences of transposition. If retroelements have played a significant role in adaptive mutation in natural populations, then plant geneticists may be able to accelerate and direct the process to generate new resistant alleles. New insertion sites would be “tagged” by the element and it may be possible to distinguish these sites from pre-existing loci by competitive hybridization schemes. It should then be possible to clone and characterize the disrupted loci. In addition, if the element has contributed to genotypic changes that have persisted under the pressure of selection, then important loci may be closely linked to the element, a feature that may make it easier to map and isolate coding regions by element-anchored polymorphisms.

EXAMPLE 11 Modification of SIRE-1 Vectors to Effect Directed Integration

Retroviral integration systems show little target site specificity, and random insertions into a target cell genome may have undesirable consequences: integration near cellular proto-oncogenes may lead to ectopic gene activation and tumor production (Shiramazu et al., 1994), and random integration may also inactivate essential or desirable genes (Coffin, 1990). Therefore, the ability to direct the integration of a plant proretrovirus to a limited region of a target plant cell genome is very desirable.

One manner by which directed integration may be effected is via “tethering” of the integration machinery to a specific target sequence. This may be accomplished by fusion of a sequence-specific DNA-binding domain to the integrase sequence of the SIRE-1 proretrovirus (Kirchner et al., 1995). The nucleotide sequence encoding the DNA-binding domain from a protein known to bind to a specific locus in the genome of a plant (i.e., a transcriptional enhancer for a gene whose expression is commercially disadvantageous) may be recombinantly inserted in-frame and just downstream from the 3′ end of the SIRE-1 nucleotide sequence encoding the carboxy-terminus of the pol region (i.e., at the carboxy-terminus of the integrase protein, which is a product of pol cleavage). The DNA-binding domain may then act to “guide” the integrase protein and the SIRE-1 polynucleotide to the genetic locus to be insertionally mutated by SIRE-1.

EXAMPLE 12 Determination of the SIRE-1 Insertion Site in the Soybean Genome

The sequence of the flanking genomic DNA from the SIRE-1 genomic clone may be used to generate probes for determination of the genomic insertion site. Restriction enzyme digests of genomic DNA from a variety of G. max cultivars, G. soja, and other plant species (for example, G. tabacina, G. canescens, and G. tormentella) will be electrophoretically fractionated on agarose gels, transferred to nylon membranes, and hybridized with the flanking DNA probe(s). If a band to which the probe(s) hybridize is polymorphic, the relation of the polymorphism to the presence of a SRRE-1 insert may be determined by hybridization with a SIRE-1 LTR-specific probe. A SIRE-1-related polymorphism among cultivars would strongly support functional transposition of the SIRE-1 family in the recent past.

The above examples support that conclusion that SIRE-1 is an endogenous family of proretroviruses whose genomic structure is based on a copia-like organization. In contrast, the genomic organization of all animal retroviruses (from vertebrates and Drosophila) is patterned after gypsy-like retrotransposons. Thus, SIRE-1 is clearly a plant retroviral element that is evolutionarily far diverged from animal retroviruses.

Neither retroviral genomes nor virions have been reported in plants, although both classes of retrotransposons are otherwise widespread in nature. Therefore, SIRE-1 is the first known plant proretrovirus. Few plant virus genomes encode an envelope protein. Those that do—rhabdoviruses and bunyaviruses—also infect animal hosts where envelope proteins sponsor viral-host cell membrane fusion. It is not known whether plant cell walls would preclude this mode of transfer.

SIRE-1 may originally have been an invertebrate retrovirus. Its ability to integrate into plant genomes and the presence of envelope protein-encoding regions suggests the possibility that at one time it may have served as a “shuttle vector” between and among animal and plant hosts. Judging by its copy number it has clearly been successful in G. max.

The overall restriction site homogeneity of family members, the presence of long, uninterrupted ORFs within and adjacent to the retroviral insert, the strong homologies of the env, gag, int, RT and RH domains to those from known retrotransposons, and the near-identity of the LTRs indicate that SIRE-1 is not an evolutionary relic, but an active proretrovirus. As such, it may be utilized to influence the organization and expression of soybean and possibly other plant genomes.

From the foregoing it may be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention (as set out in the appended claims).

REFERENCES CITED

The following publications which were cited in the specification are incorporated in their entirety by reference herein.

Ahlquist, P., R. French, J. J. Bujarski. Molecular studies of Brome mosaic virus using infectious transcripts from cloned cDNA. Adv. Virus Res. 32:214-242 (1987).

Ahlquist, P., R. F. Pacha. Gene amplification and expression by RNA viruses and potential for further application to plant gene transfer. Physiol. Plant. 79:163-167 (1990).

Altenbach, S. B., K. W. Pearson, G. Meeker, L. C. Staraci, and S. S. M. Sun. Enhancement of the methionine content of seed proteins by the expression of a chimeric gene encoding a methionine-rich protein in transgenic plants. Plant Mol. Biol. 13:513 (1989).

Amberger, L. A., R. G. Palmer and R. C. Shoemaker. Analysis of culture-induced variation in soybean. Crop Sci. 32:1103-1108 (1992).

Ashfield, T., N. T. Keen, R. I. Buzzell, R. W. Innes. 1995. Soybean resistance genes specific for different Pseudomonas syringae avirulence genes are allelic, or closely linked, at the RPGI locus. Genetics 141:1597.

Baltazar, M B, Mansur, L. 1992. Identification of restriction fragment length polymorphisms to map soybean cyst nematode resistance genes in soybean. Soybean Genet. Newslett. 19: 120.

Beachy, R. N. 1990. Plant transformation to confer resistance against virus infection, in Gene Manipulation in Plant Improvement, Vol. 2, Gustafson, J. P., ed., Plenum Press, New York.

Berg, D. E. and M. M. Howe, eds. 1989. Mobile DNA, ASM Washington, D.C.

Bernard, R. L., Cremeens, C. R. 1971. A gene for general resistance to downy mildew of soybeans. J. Hered. 62:359.

Bi, Y.-A. and H. M. Laten. 1996. Sequence analysis of a cDNA containing the gag and prot regions of the soybean retrovirus-like element, SIRE-1. Plant Mol. Biol. 30:1315.

Boeke, J. D. 1989. Transposable elements in Saccharomyces cerevisiae. In Mobile DNA, D. E. Berg and M. M. Howe, eds., ASM, Washington, D.C., pp. 335-374.

Boerma, H R, Harris, B B, Kuhn, C W. 1975. Inheritance of resistance to cowpea chlorotic mottle virus in soybeans, Crop Sci. 15: 849.

Brettell, R. I. S. and E. S. Dennis. 1991. Reactivation of a silent Ac following tissue culture is associated with heritable alterations in its methylation pattern. Mol. Gen. Genet. 229, 365-372.

Brisson, N., J. Paszkowski, J. R. Penswick, B. Gronenborn, I. Potrykus, T. Hohn. 1984. Expression of a bacterial gene in plants by using a viral vector. Nature 310, 511-14.

Britten, R. J., Proc. Natl. Acad. Sci. USA 92, 599 (1995).

Britten, R. J., T. J. McCormack, T. L. Mears, E. H. Davidson, J. Mol. Evol. 40, 13 (1995).

Brunke, K. J. and R. L. Meeusen. 1991. Insect control with genetically engineered crops. Trends Biotechnol. 9, 197.

Boutin, S, Ansari, H, Concibido, V, Denny, R, Orf, J, Young, N. 1992. RFLP analysis of cyst nematode resistance in soybeans. Soybean Genet. Newslett. 19: 123.

Burmeister, M. and H. Lehrach. Trends Genet. 12:389 (1996).

Bureau, T. E., S. E. White, S. R. Wessler, Cell 77:479 (1994).

Buss, G. R., Roane, C. W., Tolin, S. A., Vinardi, T. A. 1985. A second dominant gene for resistance to peanut mottle virus in soybeans. Crop Sci. 25:314.

Cal, H. and M. Levine. 1995. Modulation of enhancer-promoter interactions by insulators in the Drosophila embryo. Nature 376:533-536.

Casacuberta, J. M., S. Vemhettes and M.-A. Grandbastien. 1995. Sequence variability within the tobacco retrotransposon Tnt1 population. EMBO J. 14, 2670-2678.

Caverec, L. and T. Heidmann. 1993. The Drosophila copia retrotransposon contains binding sites for transcriptional regulation by homeoproteins. Nucl. Acids Res. 21, 5041-5049.

Cavarec, L., S. Jensen and T. Heidmann. 1994. Identification of a strong transcriptional activator for the copia retrotransposon responsible for its differential expression in Drosophila hydei and melanogaster cell lines. Biochem. Biophys. Res. Commun. 20-31, 392-399.

Chambers, P., C. R. Pringle, A. J. Easton, J. Gen. Virol. 71, 3075 (1990).

Chan, D. C., D. Fass, J. M. Berger, P. S. Kim, Cell 89, 263 (1997).

Chen, P., Buss, G. R., Tolin, S. A. 1993. Resistance to soybean mosaic virus conferred by two independent dominant genes in PI 486355. J. Hered. 84: 25.

Choi, S.-Y. and D. V. Faller. 1994. The long terminal repeats of a murine retrovirus encode a transactivator for cellular genes. J. Biol. Chem. 269, 19691-19694.

Dahlberg, J. E., R. C. Sawyer, J. M. Taylor, A. J. Faras, W. E. Levinson, H. M. Goodman, and J. M. Bishop. 1974. Transcription of DNA from the 70S RNA of Rous sarcoma virus. 1. Identification of a specific 4S RNA which serves as primer. J. Virol. 13:1126-1133.

Dalgleish, A. G., P. C. L. Beverly, P. R. Clapham, D. H. Crawford, M. F. Greaves, and R. A. Weiss. 1984. The CD4 antigen is an essential component of the receptor for the AIDS retrovirus. Nature 312, 763-767.

Day, A. G., E. R. Bejarano, K. W. Buck, M. Burrell, and C. P. Lichtenstein. 1991. Expression of an antisense viral gene in transgenic tobacco confers resistance to the DNA virus tomato golden mosaic virus. Proc. Natl. Acad. Sci. U.S.A. 88, 6721.

Deleage, G., and B. Roux, Prot. Engng. 1, 289 (1987).

della-Cioppa, G., S. C. Bauer, M. L. Taylor, D. E. Rochester, B. K. Klein, D. M. Shah, R. T. Fraley, and G. M. Kishore. 1987. Targeting a herbicide resistant enzyme from Escherichia coli to chloroplasts of higher plants. Bio/Technology 5, 579.

Di, R., V. Purcell, G. B. Collins, S. A. Ghabrial. 1996. Production of transgenic soybean lines expressing the bean pod mottle virus coat protein precursor gene. Plant Cell. Reports 15:746.

Dickinson, C. D., M. P. Scott, E. H. A. Hussein, P. Argos, and N. C. Nielsen. 1990. Effect of structural modifications on the assembly of a glycinin subunit. Plant Cell. 2, 403.

Diers, B. W., Mansur, L., Imsande, J., Shoemaker, R. C. 1992. Mapping phytophthora resistance loci in soybean with resistance fragment length polymorphism markers. Crop Sci. 32: 377.

Eickbush, T. H., in The Evolutionary Biology of Viruses, S. S. Morse, Ed. (Raven Press, New York, 1994) pp. 121-157.

Engels, W. R. 1989. P elements in Drosophila melanogaster. In Mobile DNA, D. E. Berg and M. Howe, eds., ASM, Washington, D. C., pp. 437-484.

Fass, D., S. C. Harrison, P. S. Kim, Nature Struct. Biol. 3, 465 (1996).

Federoff, N. V. 1989. Maize transposable elements. In Mobile DNA, D. E. Berg and M. M. Howe, eds., ASM Washington, D. C., pp. 375-41 1.

Felder, H., A. Herzceg, Y. deChastonay, P. Aeby, H. Tobler, F. Muller, Gene 149, 219 (1994)

Finnegan, D. J. 1989. Eukaryotic transposable elements and genome evolution. Trends Genet. 5, 103107.

Flavell, A. J., V. Jackson, M. P. Iqbal, I. Riach, S. Waddell, Mol. Gen. Genet. 246, 65 (1995).

Flavell, A. J., D. B. Smith and A. Kumar. 1992. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol. Gen. Genet. 231, 233-242.

Fontenot, J. D., N. Tjandra, C. Ho, P. C. Andrews, R. C. Montelaro, J. Biomol. Struct. Dynam. 11, 821 (1994).

Freytag, A. H., A. P. Rao-Arelli, S. C. Anand, I. A. Wrather and L. D. Owens. 1989. Somaclonal variation in soybean plants regenerated from tissue culture. Plant Cell Rep. 8, 199-202.

Friesen, P. D., and M. S. Nissen, Mol. Cell. Biol. 10, 3067 (1990).

Gallaher, W. R., J. M. Ball, R. F. Garry, A. M. Martin-Amedee, R. C. Montelaro, AIDS Res. Hum. Retroviruses 11, 191 (1995).

Gallaher, W. R., J. M. Ball, R. F. Garry, M. C. Griffin, R. C. Montelaro, AIDS Res. Hum. Retroviruses 5, 431 (1989).

Georgiev, P. G. and V. G. Corces. 1995. The su(Hw) protein bound to gypsy sequences in one chromosome can repress enhancer-promoter interactions in the paired gene located on the other homolog. Proc. Natl. Acad. Sci. USA 92. 5184-5 1 S&

Georjon, C., and G. Deleage, Comput. Applic. Biosci. 11, 681 (1995).

Georjon, C., and G. Deleage, Prot. Engng. 7, 157 (1994).

Gever, P. K. and V. G. Corces. 1992. DNA position-specific repression of transcription by a Drosophila zinc finger protein. Genes Dev. 6, 1865-1873).

Gibrat, J. F., J. Garnier, B. Robson, J. Mol. Biol. 198, 425 (1987).

Gijzen, M., T. MacGregor, M. Bhattacharyya, R. Buzzell. 1996. Temperature-induced susceptibility to Phytophthora sojae in soybean isolines carrying different RPS genes. Physiol. Mol. Plant Path. 48:209.

Golemboski, D. B., G. P. Lomonossoff, and M. Zaitlin. 1990. Plants transformed with a tobacco mosaic virus nonstructural gene sequence are resistant to the virus. Proc. Natl. Acad. Sci. U.S.A. 87, 6311.

Grandbastien, M.-A. 1992. Retroelements in higher plants. Trends Genet. 8, 103-108.

Grandbastien, M.-A., A. Spielmann and M. Caboche. 1989. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337, 376-380.

Graybosch, R. A., N. E. Edge and X. Delannay. 1987. Somaclonal variation in soybean plants regenerated from cotyledonary node tissue culture system. Crop Sci. 27, 803-806.

Gresshoff, P. M. and D. Landau-Ellis. 1994. Molecular mapping of soybean nodulation genes. In Plant Genome Analysis, P. Gresshoff, ed., CRC Press, Boca Raton, pp. 97-112.

Groose, R. W. and R. G. Palmer. 1987. New mutations in a genetically unstable line of soybeans. Soybean Genet. Newsl. 14, 164-1610.

Groose, R-W., H. D. Weigelt and R-G. Palmer. 1988. Somatic analysis of unstable mutation for anthocyanin pigmentation in soybean. 1. Heredity 79, 263-267.

Hagen, G., and T. Guilfoyle. 1985. Rapid induction of selective transcription by auxins. Mol. Cell Biol. 5, 1197.

Harlow, E., and D. Lane. 1985. Antibodies: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

Hartwig, E. E., Bromfield, K. R. 1983. Relationships among three genes conferring specific resistance to rust in soybeans. Crop Sci. 23: 237.

Haughn, G. W., et al. 1988. Mol. Gen. Genet. 211, 266.

Hemenway, C., R.-X. Fang, W. K. Kaniewski, N.-H. Chua, and N. E. Tumer. 1988. Analysis of the mechanism of insect resistance engineered into tobacco. Nature 330, 160.

Hill, K. K., N. Jarvis-Eagan, E. L. Halk, K. J. Krahn, L. W. Liao, R. S. Mathewson, D. J. Merlo, S. E. Nelson, K. E. Rashka, and L. S. Loesch-Fries. 1991. The development of virus-resistant alfalfa, Medicago sativa L. Bio/Technology 9, 373.

Hirochika, H. 1993. Activation of tobacco retrotransposons during tissue culture. EMBO J. 12, 2521-2528.

Hoffman, L. M., D. D. Donaldson, and E. M. Herman. 1988. A modified storage protein is synthesized, processed, and degraded in the seed of transgenic plants. Plant Mol. Biol. 11, 717.

Hofmann, K., and W. Stoffel, Biol. Chem. Hoppe-Seyler 347, 166 (1993).

Horsch, R. B., et al. 1984. Science 223, 496.

Hsu, H. T., and R. H. Lawson. 1991. Direct tissue blotting for detection of tomato spotted wilt virus in Impatiens. Plant Dis. 75, 292.

Hu, W., O. P. Das and J. Messing. 1995. Zeon-1, a member of a new maize retrotransposon family. Mol.Gen. Genet. 248, 471-480.

Hunter, E., and R. Swanstrom, Curr. Top. Microbiol. Immunol. 157, 187 (1990)

Hutchinson III, C. A., S. C. Hardies, D. D. Loeb, W. R. Shehee & M. H. Edgell. 1989. LINES and related retroposons: long interspersed repeated sequences in the eucaryotic genome. In Mobile DNA, D. E. Berg and M. M. Howe, eds., ASM, Washington, D. C., pp.593-617.

Inouye, S., S. Yuki, K. Saigo, Eur. J. Biochem. 154, 417 (1986).

Johns, M. A., J. Mottinger and M. Freeling. 1985. A low copy number, copia-like transposon in maize. EMBO J. 4, 1093-1102.

Kaeppler, S. M. and R. L. Phillips. 1993. Tissue culture-induced DNA methylation variation in maize. Proc. Natl. Acad. Sci. USA 90, 8773-8776.

Kasuga, T, Gijzen, NC, Buzzelli, R, Bhattacharyya, M. 1996. Isolation and mapping of amplified fragment length polymorphisms (AFLP) DNA markers that are linked to the RPS I locus of soybean. (Abstract) Plant Genome IV, San Diego, 1996.

Katz, R. A. and J. E. Jentoft. 1989. What is the role of the Cys-His motif in retroviral nucleocapsid (NC) proteins? Bioessays II, 176-18 1.

Keen, N T, Buzzell, R I. 1991. New disease resistance genes in soybean against Pseudomonas syringae pv glycinea: evidence that one of them interacts with a bacterial elicitor. Theor. Appl. Genet. 81: 133.

Keim, P, Schupp, J M, Ferreira, A, Zhu, T, Shi, L, Travis, S E, Clayton, K, Webb, D M. 1996. A high density soybean genetic map using RFLP, RAPD, and AFLP genetic markers. (Abstract) Plant Genome IV, San Diego, 1996.

Kilen, T C, Hartwig, E E. Identification of single genes controlling resistance to stern canker in soybean. Crop Sci. 27: 863.

Kim, A., C. Terzian, P. Santamaria, A. Pelisson, N. Prudhomme, A. Bucheton, Proc. Natl. Acad. Sci. USA 91, 1285 (1994).

Kina, C. C. 1992. Modular transposition and the dynamic structure of eukaryotic regulatory evolution. Genetica 86, 127-142.

Laten, H. M. and R. O. Morris. 1993. SIRE-1, a long, interspersed repetitive DNA element from soybean with weak sequence similarity to retrotransposons: initial characterization and partial sequence. Gene 134, 153-159.

Lee, S-H, Tamulonis, J, Bailey, M, Man, R, Ashley, D, Parrott, W, Boerma, R, Carter, Jr, T, Shipe, E, Hussey, R. 1996. Molecular markers associated with soybean seed protein and oil across populations and locations. (Abstract) Plant Genome IV, San Diego, 1996.

Lee, W. S., J. T. C. Tzen, J. C. Kridl, S. E. Radke, and A. H. C. Huang. 1991. Maize oleosin is correctly targeted to seed oil bodies in Brassica napus transformed with the maize oleosin gene. Proc. Natl. Acad. Sci. U.S.A. 88, 6181.

Levin, J. M., B. Robson, J. Garnier, FEBS Lett. 205, 303 (1986).

Lim, J. K. and M. J. Simmons. 1994. Gross chromosomal rearrangements mediated by transposable elements in Drosophila melanogaster. Bioessays 16, 269-275.

Lohnes, D G, Bernard, R I. 1992. Inheritance of resistance to powdery mildew in soybeans. Plant Disease 76: 964.

Lohning, C. and M. Ciriacy. 1994. The TYE7 gene of Saccharomyces cerevisiae encodes a putative bHLH-LZ transcription factor required for Ty1-mediated gene expression. Yeast 10, 1329-1339.

Lupas, A., M. Van Dyke, J. Stock, Science 252, 1162 (1991)

Luzzi, B M, Boerma, H R, Hussey, R S. 1994. A gene for resistance to the soybean root-knot nematode in soybean. J. Hered. 85: 484.

Luzzi, B M, Boerma, H R, Hussey, R S. 1994. Inheritance of resistance to the soybean root-knot nematode in soybean. Crop Sci. 34: 1240.

Ma, G., P. Chen, G. R. Buss, S. A. Tolin. 1995. Genetic characteristics of two genes for resistance to soybean mosaic virus in P1486355 soybean. Theor. Appl. Genetics 91:907.

Mansky, L. M., D. P. Durand and J. H. Ell. 1991. Effects of temperature on the maintenance of resistance to soybean mosaic virus in soybean. Phytopathol. 8 1, 53 5-53) 8.

Matthews, R. E. F., Plant Virology (Academic Press, New York, 1991).

McClintock, B. 1984. The significance of responses of the genome to challenge. Science 226, 792-801.

McDonald, J. F. 1990. Evolution and consequences of transposable elements. Curr. Opin. Genet. Devel. 3, 855-864.

McDonald, J. F. 1990. Macroevolution and retroviral elements. BioScience 40, 183-191.

McDonald, J. F., D. J. Strand, M. R. Brown, S. M. Paskewitz, A. K. Csink and S. H. Voss. 1988. Evidence of hostmediated regulation of retroviral element expression at the posttranscriptional level. In Eukaryotic Transposable Elements as Mutagenic Agents, M. E. Lambert, J. F. McDonald and I. B. Weinstein, eds., Cold Spring Harbor Laboratory, New York, pp. 219-234.

McEntee, K. and V. A. Bradshaw. 1988. Effects of DNA damage on transcription and transposition of Ty retrotransposons of yeast. In Eukaryotic Transposable Elements as Mutagenic Agents, M. E. Lambert, J. F. McDonald and I. B. Weinstein, eds., Cold Spring Harbor Laboratory, New York, pp. 245-253.

Mellentin-Michelotti, J., S. John, W. D. Pennie, T. Williams and G. L. Hager. 1994. The 5′ enhancer of the mouse mammary tumor virus long terminal repeat contains a functional AP-2 element. J. Biol. Chem. 269, 31983-31990.

Moreira, M A, Barros, E G, Sediyama, C S, Sediyama, T. 1996. Breeding soybean for high quality seeds assisted by molecular markers. (Abstract) Plant Genome IV, San Diego, 1996.

Murphy, J. E., and S. P. Goff. 1988. Construction and analysis of deletion mutations in the U5 region of Moloney murine leukemia virus: effects on RNA packaging and reverse transcription. J. Virol. 63, 319-327.

Mushegian, A. R. and E. V. Koonin, Arch Virol. 133, 239 (1993).

Nathan, M., L. M. Mertz and D. K. Fox. 1995. Optimizing long RT-PCR. Focus 17, 78-80.

Navot, N., R. Ber, and H. Czosnek. 1989. Rapid detection of tomato yellow leaf curl virus in squashes of plant and insect vectors. Phytopathology 79, 562.

Nelson, R. S., S. M. McCormick, X. Delannay, P. Dube, J. Layton, E. J. Anderson, M. Kaniewska, R. K. Proksch, R. B. Horsch, S. G. Rogers, R. T. Fraley, and R. N. Beachy. 1993. Virus tolerance, plant growth, and field performance of transgenic tomato plants expressing coat protein from tobacco mosaic virus. Bio/Technology 6, 403.

Ngeleka, K, Smith O D. 1993. Inheritance of stem canker resistance in soybean cultivars Crockett and Dowling. Crop Sci. 33: 67.

Padgette, S. R., N. B. Taylor, D. L. Nida, M. R. Bailey, J. MacDonald, L. R. Holden, R. L. Fuchs. 1996. The composition of glyphosphate-tolerant soybean seeds is equivalent to that of conventional soybeans. J. Nutr. 126:702.

Palmgren, M. G. 1994. Capturing of host DNA by a plant retroelement: Bs I encodes plasma membrane H+-ATPase domains. Plant Mol. Blol. 25, 137-140.

Patience, C., D. A. Wilkenson, R. A. Weiss, Trends Genet. 13, 116 (1997).

Paquin, E. and V. M. Williamson. 1988. Effect of temperature on Ty transposition. In Eukaryotic Transposable Elements as Mutagenic Agents, M. E. Lambert, I. F. McDonald and I. B. Weinstein, eds., Cold Spring Harbor Laboratory, New York, pp. 235-244.

Pearl, L. H. and W. R. Taylor. 1987. A structural model for the retroviral proteases. Nature 329, 351354.

Perlak, F. J., R. L. Fuchs, D. A. Dean, S. L. McPherson, and D. A. Fischoff. 1991. Modification of the coding sequence enhances plant expression of insect control protein genes. Proc. Natl. Acad. Sci. U.S.A. 88, 3324.

Peschke, V. M. and R. L. Phillips. 1991. Activation of the maize transposable element Suppressor-mutator (Spm) in tissue culture. Theor. Appl. Genet. 81, 90-97.

Peschke, V. M., R. L. Phillips and B. G. Gengenbach. 1991. Genetic and molecular analysis of tissue culture-derived Ac elements. Theor. Appl. Genet. 821, 121-129.

Phillips, D, Boerma, B R. 1982. Two genes for resistance to race S of Cercospora sojina in soybeans. Phytopathol. 72: 764.

Pinter, A., and W. J. Honnen, J. Virology 62, 1016 (1988).

Pouteau, S., M.-A. Grandbastien and M. Boccara. 1994. Microbial elicitors of plant defense responses activate transcription of a retrotransposon. Plant J. 5, 535-542.

Prabhu, R, Doubler, T W, Chang, SIC, Lightfoot, D A. 1996. Development of sequence characterized amplified regions (SCARs) for marker-assisted selection of soybean lines resistant to sudden death syndrome. (Abstract) Plant Genome IV, San Diego, 1996.

Qian, D., F. L. Allen, G. Stacey, P. M. Gresshoff. 1996. Plant genetic study of restricted nodulation in soybean. Crop Sci. 36(2): 243-49.

Rao-Arelli, A P, Anand, S C, Wrather, A. 1992, Soybean resistance to soybean cyst nematode race 3 is conditioned by an additional dominant gene. Crop Sci. 32: 862.

Rezaian, M. A., K. G. M. Skene, and J. G. Ellis. 1988. Antisense RNAs of cucumber mosaic virus in transgenic plants assessed for control of the virus. Plant Mol. Biol. 11, 463.

Rio, D. C. 1990. Molecular mechanisms regulating Drosophila P element transposition. Annu. Rev. Genet. 24, 543-578.

Robertson, H. D., S. H. Howell, M. Zaitlin, and R. L. Malmberg, eds. 1983. “Plant infectious agents” in Viruses, Viroids, Virusoids, and Satellites. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

Robins, D. M. and L. C. Samuelson. 1993. Retrotransposons and the evolution of mammalian gene expression. In Transposable Elements and Evolution, J. F. McDonald, ed., Kluwer, Dordrecht, pp. 515.

Roth, E. J., B. L. Frazier, N. R. Apuya and K. G. Lark. 1989. Genetic variation in an inbred plant: variation in tissue cultures of soybean (Glycine max (L.) Merrill). Genetics 12: 359-368.

Saigo, K., W. Kugiyama, Y. Matsuo, S. Inouye, K. Yoshioka, S. Yuki, Nature 312, 659 (1984).

Sambrook, J., E. F. Fritsch and T. Maniatis. 1989. Molecular Cloning. Cold Spring Harbor Laboratory: New York.

Sandmeyer, S. B., L. J. Hansen and D. L. Chalker. 1990. Integration-specificity of retrotransposons and retroviruses. Annu. Rev. Genet. 24, 491-518.

Sanger, F., S. Nicklen and A. R. Coulson. 1977. DNA sequencing with chain terminating inhibitors. Proc. Nat. Acad. Sci. USA 74, 5463-5467.

SanMiguel, P., A. Tikhonov, Y.-K. Jin, N, Motchoulskaia, D. Zakharov, A. Melake-Berhan, P. S. Springer, K. J. Edwards, M. Lee, Z. Avramova, J. L. Bennetzen, Science 274, 765 (1996).

Schwarz-Sommer, Z. and H. Saedler. 1987. Can plant transposable elements generate novel regulatory systems? Mol. Gen. Genet. 209, 207-209.

Schwarz-Sommer. Z. and H. Saedler. 1988. Transposition and retrotransposition in plants. In Plant Transposable Elements, 0. Nelson, ed. Plenum Press: New York, pp. 175-187.

Shah, D. M. et al. 1986. Science 233, 478.

Shapiro, J. A. 1983. Mobile Genetic Elements. New York: Academic Press.

Shapiro, J. A. 1992. Natural genetic engineering in evolution. Genetica 86, 99-111.

Sheridan, M. A. and R. G. Palmer. 1977. The effect of temperature on an unstable gene in soybeans. J. Hered. 68, 17-22.

Shih, C. C., J. P. Stoye, and J. M. Coffin. 1988. Highly preferred targets for retrovirus integration. Cell 53, 531-537.

Shoemaker, R, S. Zhao, V. Kanazin, L. Marek. 1996. Phytophthora root rot resistance gene mapping in soybean. (Abstract) Plant Genome IV, San Diego, 1996.

Shoemaker, R. C., L. A. Amberger, R. G. Palmer, L. Oglesby and J. P. Ranch. 1991. Effect of 2,4 dichlorophenoxyacetic acid concentration on somatic embryogenesis and heritable variation in soybean [Glycine max (L) Merr.]. In Vitro Cell. Dev. Biol. 27P, 84-88.

Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503.

Switzer, W. M. and W. Heneine. 1995. Rapid screening of open reading frames by protein synthesis with an in vitro transcription and translation system. Biotech. 18, 244-1-48.

Takahashi, R., and S. Asanuma. 1996. Association of T gene with chilling tolerance in soybean. Crop Sci. 36:559.

Tanda, S., J. L. Mullor, V. G. Corces, Mol. Cell. Biol. 14, 5392 (1994).

Titus, D. E. 1991. Promega Protocols and Applications Guide. Madison, Wis.

H. B. Urnovitz and W. H. Murphy, Clin. Microbiol. Rev. 9, 72 (1996).

Vaeck, M., A. Reynaerts, H. Hofte, S. Jansens, M. DeBeuckeleer, C. Dean, M. Zabeau, M. Van Montagu, and J. Leemans. 1987. Transgenic plants protected from insect attack. Nature 328, 33.

Varmus, H., and P. Brown, in Mobile DNA, D. E. Berg and M. M. Howe, Eds. (ASM, Washington, D.C., 1989) pp 53-108.

Varmus, H. E. 1982. Form and function of retroviral proviruses. Science 216, 812-821.

Varmus, H. and P. Brown. 1989. Retroviruses. In Mobile DNA, D. E. Berg and M. M. Howe, eds. pp.53-108.

Voytas, D. F., M. P. Cummings, A. Konieczny, F. M. Ausubel and S. R. Rodermel. 1992. copia-like retrotransposons are ubiquitous among plants. Proc. Natl. Acad. Sci. USA 89, 7124-7128.

Watson, J. D., N. H. Hopkins, J. W. Roberts, J. A. Steitz, and A. M. Weiner. 1987. Molecular Biology of the Gene. Menlo Park: Benjamin/Cummings Publishing.

Waugh, R. and J. W. S. Brown. 1991. Plant gene structure and expression. In Plant Genetic Engineering, D. Gierson, ed., Chapman and Hall, New York, pp. 1-37.

Weil, C. F. and S. R. Wessler. The effects of plant transposable element insertions on transcription initiation and RNA processing. 1990. Annu. Rev. Plant Physiol. Plant Mol. Biol. 41, 527-552.

White, S. E., L. F. Habera and S. R. Wessler. 1994. Retrotransposons in the flanking regions of normal plant genes: A role for copia-like elements in the evolution of gene structure and expression. Proc. Nad. Acad. Sci. USA 91, 11792-11796.

Williamson, M. P., Biochem. J. 297, 249 (1994).

Wilson, I. B. H., Y. Gavel, G. von Heijne, Biochem. J. 275, 529 (1991).

Wu, S. C., Q. Lu, A. L. Kriz, J. E. Harper. 1995. Identification of cDNA clones corresponding to two inducible nitrate reductase genes in soybean—analysis in wild-type and NR(1) mutant. Plant Mol. Biol. 29:491-506.

Young, N D. 1996. Genome analysis of soybean cyst nematode resistance in soybean. (Abstract) Plant Genome IV, San Diego, 1996.

Yu, Y. G., M. A.S. Maroof, G. R. Buss. 1996. Divergence and allelomorphic relationship of a soybean virus resistance gene based on tightly linked DNA microsatellite and RFLP markers. Theor. Appl. Genetics 92:64.

86 1 22 DNA Artificial Sequence primer 1 tnttngatcg kgtncartgc tg 22 2 776 DNA Glycine max misc_feature SIRE-1 fragment from Glycine max genomic DNA 2 tattggatcg ggtgcagtgc tgtttttggc aggaacaaat tatgtcatgg ttgttctgcc 60 agcagattta tgattaaatc caagtcctct ctggtttcca acattcttcc caagctgtag 120 cacctcatca agcaaatttg agcctttatt cagcatcttt attgattttg tcatgttttc 180 cagtttagag ttcagaaaac caatttctcc tttaagttca gagatttcct cttcatgtgc 240 ctccttctca gcctccagat ttgcaatgac cttctttagt tgtgcttctt gctgaagaat 300 cttctcactt ttgatgcata gttctctata ggatatagca agctcatcaa aagtgatttc 360 actatctgta tcacttgaat cttcagcaga ttcaaatctc ccagtgagtg cattcacatc 420 tctgtcagaa tcacttcttg ttcactctct gtatcatcag accgacatac agaaagtcct 480 ttcctctgct tcttgagatg agtgggacat tcagctttga tgtgtccata gccttcacac 540 ccatggcatt gaattccttt gctgtgactg ggcttttcat ctgacctttt ctggtattca 600 ctacctttcc tgatgtcgaa agggatgttc cggacatgtg gtttctgcct cctgtccatt 660 ctgttcagca ctttgttgaa ctgttttcca aggagcacaa ctgcgttagt cagaccttca 720 tcagtatcca ggtcatactc atcttcttct ccttcagcac tgcacccgat ccaata 776 3 2417 DNA Glycine max misc_feature SIRE-1 cDNA clone 3 tccggtccct ggcttggtag cccccagatg taggtgaggt tgcaccgaac tgggttaaca 60 attctcttgt gttagttact tgtttaatct gttcatacag tcaaacataa tctgcatgtt 120 ctgaagcgtg atgtcgtgac atccggtacg acatctgtca ttggtatcag aatttcaatt 180 ggtatcagag caggcactcg aattcactga gtgagatcta gggagataaa ttctgatgaa 240 catggagaaa gaaggaggac cagtgaacag accaccaatt ctggatggaa ccaactatga 300 atactggaaa gcaaggatgg tggccttcct caaatcactg gatagcagaa cctggaaagc 360 tgtcatcaaa gactgggaac atcccaagat gctggacaca gaaggaaagc ccactgatgg 420 attgaagcca gaagaagact ggactaaaga agaagacgaa ttggcacttg gaaactccaa 480 agctttgaat gctctattca atggagttga caagaatatc ttcagactga tcaacacatg 540 cacagtggcc aaggatgcat gggagatcct gaaaaccact catgaaggaa cctccaaagt 600 gaagatgtcc agattgcaac tattggccac aaaattcgaa aatctgaaga tgaaggagga 660 agagtgtatt catgactttc acatgaacat tcttgaaatt gccaatgctt gcactgcctt 720 gggagaaaga atgactgatg aaaagctggt gagaaagatc ctcagatcct tgcctaagag 780 atttgacatg aaagtcactg caatagagga ggcccaagac atttgcaacc tgagagtaga 840 tgaactcatt ggttcccttc aaacctttga gctaggactc tcggatagga ctgaaaagaa 900 gagcaagaat ctggcgttcg tgtccaatga tgaaggagaa gaagatgagt atgacctgga 960 tacagatgaa ggtctgacta atgcagttgt gctccttgga aaacagttca acaaagtgct 1020 gaacagaatg gacaggaggc agaaaccaca tgtccggaac atccctttcg acatcaggaa 1080 aggtagtgaa taccagaaaa ggtcagatga aaagcccagt cacagcaaag gatttcaatg 1140 ccatgggtgt gaaggctatg gacacatcaa agctgaatgt cccactcatc tcaagaagca 1200 gaggaaagga ctttctgtat gtcggtctga tgatacagag agtgaacaag aaagtgattc 1260 tgacagagat gtgaatgcac tcactgggag atttgaatct gctgaagatt caagtgatac 1320 agacagtgaa atcacttttg atgagcttgc tacatcctat agagaactat gcatcaaaag 1380 tgagaagatt cttcagcaag aagcacaact gaagaaggtc attgcaaatc tggaggctga 1440 gaaggaggca catgaagagg agatctctga gcttaaagga gaagttggtt ttctgaactc 1500 taaactggaa aacatgacaa aatcaataaa gatgctgaat aaaggctcag atatgcttga 1560 tgaggtgcta cagcttggga agaatgttgg aaaccagaga ggacttgggt ttaatcataa 1620 atctgctggc agaataacca tgacagaatt tgttcctgcc aaaatcagca ctggagccac 1680 gatgtcacaa catcggtctc gacatcatgg aacgcagcag aaaaagagta aaagaaagaa 1740 gtggaggtgt cactactgtg gcaagtatgg tcacataaag cccttttgct atcatctaca 1800 tggccatcca catcatggaa ctcaaagtag cagcagcaga aggaagatga tgtgggttcc 1860 aaaacacaag attgtcagtc ttgttgttca tacttcactt agagcatcag ctaaggaaga 1920 ttggtaccta gatagcggct gttccagaca catgacagga gtcaaagaat ttctggtgaa 1980 cattgaaccc tgctccacta gctatgtgac atttggagat ggctctaaag gaaagatcac 2040 tggaatggga aagctagtcc atgatggact tcgttatgtc aaggaataag atcgggctgc 2100 acaatgcaca aggcaagata aaatgtcaaa tgaagaattg aagctgcagg atccatgatg 2160 tcggatacaa tgtccaggac atcctgcccg aaaatactgg agttgctgca caatgcacaa 2220 ggcaagataa aagaagtgaa gctgcaggat ccacgatgtc ggatacgatg tccaggacat 2280 ctggcccgaa aatactggac acataaatct gttatatctt taacagatta ttgtgcagtt 2340 agcaacaggt tagacgatct atctttagga acgaactctt ctagttccgg aattcgagct 2400 cggtacccgg ggatcct 2417 4 14 PRT Glycine max 4 Cys His Gly Cys Glu Gly Tyr Gly His Ile Lys Ala Glu Cys 1 5 10 5 10 PRT Glycine max 5 Leu Asp Ser Gly Cys Ser Arg His Met Thr 1 5 10 6 22 DNA Glycine max 6 tggtatcaga gcaggcactc ga 22 7 17 DNA Glycine max misc_feature 3′ end of SIRE-1 element (sequence is identified in the 5′ to 3′ direction in the sequence listing and in the 3′ to 5′ direction in Figure 12 7 actttaagac tatggtt 17 8 4224 DNA Glycine max misc_feature SIRE-1 genomic DNA clone 8 gctcgcggcc gcgagctcta atacgactca ctatagggcg tcgactcgat cttgttgatg 60 ataaagttat cacactggag catgttgaca ctgaggaaca aatagcagat attttcacaa 120 aggcattgga tgcaaatcag tttgaaaaac tgaggggcaa gctgggcatt tgtctgctag 180 aggatttata gcaattactt ttatctgaac gtgcttaaac gttaatagcg cgttctctac 240 tgggccaaaa caaattcgac cgttgcttca cacgtccctc tacattcctc attcaaactc 300 atattttcgt ggtaatctcg ttttcagcat tccccaacag ctctcagaga tttacgaaac 360 cattccaaag gctctgcttc tccatggcta cctcaccaaa agatacttca tctcctggtt 420 caccctctgt accatcatct ccatcatcca ccaaagcacc atcaaaccag gaacaacctg 480 aattccatat ccaacccata caaatgattc ctggtctagc ccctgttcct gagaaactgg 540 tccccataag acaacaggga gtgaagattt ctgaaaaccc tagcattgca acaagtccta 600 gggaattgac acgggagatg gataagaaga tccgcagtat tgtgagtagt attctgaaaa 660 atgcttctgt ccctgatgct gataaagatg ttccaacatc ttccacccca aatgctgaag 720 tcctctcttc atccagtaaa gaggaatcaa cagaggaaga ggaacaagcc acagaggaga 780 cccctgcacc aagggcacca gaacctgctc caggtgacct cattgaccta gaagaagtag 840 aatctgatga ggaacccatt gccaacaagt tggcacctgg cattgcagaa agattacaaa 900 gcagaaaggg aaaaaccccc attactaggt ctggacgaat caaaactatg gcacagaaga 960 agagcacacc aatcactcct accacatcca gatggagcaa agttgcaatc ccttccaaga 1020 agaggaaaga attttcctca tctgattctg atgatgatgt cgaactagat gttcccgaca 1080 tcaagagggc caagaaatct gggaaaaagg tgcctggaaa tgtccctgat gcaccattgg 1140 acaacatttc attccactcc attggcaatg ttgaaaggtg gaaatttgta tatcaacgca 1200 gacttgcctt agaaagagaa ctgggaagag atgccttgga ttgcaaggag atcatggacc 1260 tcatcaaggg ctgctggact gctgaaaaca gtcaccaagt tgggagatgt tatgaaagcc 1320 tagtcaggga attcattgtc aacattccct ctgacataac aaacagaaag agtgatgagt 1380 atcagaaagt gtttgtcaga ggaaaatgtg ttagattctc ccctgctgta atcaacaaat 1440 acctgggcag acctactgaa ggagtggtgg atattgctgt ttctgagcat caaattgcca 1500 aggaaatcac tgccaaacaa gtccagcatt ggccaaagaa agggaagctt tctgcaggga 1560 agctaagtgt gaagtatgca atcctgcaca ggattggcgc tgcaaactgg gtacccacca 1620 atcatacttc cacagttgcc acaggtttgg gtaaatttct gtatgctgtt ggaaccaagt 1680 ccaaatttaa ttttggaaag tatatttttg atcaaactgt taagcattca gaatcatttg 1740 ctgtcaaatt acccattgcc ttcccaactg tattgtgtgg cattatgttg agtcaacatc 1800 ccaatatttt aaacaacatt gactctgtga tgaagaaaga atcggctctg tccctgcatt 1860 acaaactgtt tgaggggaca catgtcccag acattgtctc gacatcaggg aaagctgctg 1920 cttcaggtgc tgtatccaag ggatgctttg attgctgaac tcaaggacac atgcaaggtg 1980 ctggaagcaa ccatcaaagc caccacagag aagaaaatgg agctggaacg cctgatcaaa 2040 agactctcag acagtggcat tgatgatggt gaagcagctg aggaagaaga agaagccgct 2100 gaggaagaga aagatgcagc agaagataca gaatcagatg atgatgattc tgatgccacc 2160 ccatgaccat cagaccttta tttttgcttt ttactcttac tagctatagg gcatgtccct 2220 ttgaacaatt gattgctatt ggtctgtaat atttgcatgc attctacttt tgtcaaattc 2280 tgtctaaaaa ggggatatat attatgcatg attttgagta gtagatacta tgttgcaata 2340 gtatattatg cataatttat gattttgagt agtaggatac gatgtatgca tgattcatga 2400 ttttgagggg gagttgtaag tatatgattt tgagggggag tagtatctga tgatgctgat 2460 agaagatggc atggagacag ggggagcaga aagctgatgt cacgtgagat gtcttgacat 2520 cctggaaacg acttgcaact tgcagaattt tgctgtcgcc cctacagata ccgctgtgct 2580 tgattactct gataatgaaa gttgctgatc ccacttgcat aactgctcgt acctgctcag 2640 gaagtgtcta agtatgtttt agacaaaatt tgccaaaggg ggagattgtt agtgcttagc 2700 tttactgagt tttaaaagat tggctaaaat tttgttaaaa cataagcact tagacaatga 2760 aggaaagctg gagttgctgc acaggatgtc caacgttatg tcaaggaatc agattgggct 2820 ccacaatgca caaggcaaga taaaaggtca aatgaagaat tgaagctgca ggatccacga 2880 tgtcggatac aatgtccagg acatcctgcc cgaaaatact ggacacataa atctgttata 2940 tctttaacag attaatgtgc agttagcaac agatttggcg atctatcttt aggaacgaat 3000 taaaagataa ttaaagttcg aattacaaac ttgaatagtt cgttcaggga ttaaagatta 3060 aagataaaaa ctaaaagatc aaactgtatc ttttagatct ttaagtgcag atttttcagg 3120 agaatgatag atcttatcca gcgcaagatg ttgcagccca gatacgcaca ctgctatata 3180 aacatgaagg ctgcacgagt tttctaccaa gtccgggatt gaagagttat tttgtgagtt 3240 ttgggacttg agtgttttgt gagccacctt gatgttaccc taacatcaag tgttggacct 3300 gagtgtgtag agttgatctc tattgttcag agagcaatct ctggtgtgtc tttgatttat 3360 ttgtaaacac gggagagtga ttgagaggga gtgagagggg ttctcatatc taagagtggc 3420 tcttaggtag aggttgcacg ggtagtggtt aggtgagaag gttgtaaaca gtggctgtta 3480 gatcttcgaa ctaacactat tttagtggat ttcctccctg gcttggtagc ccccagatgt 3540 aggtgaggtt gcaccgaact gggttaacaa ttctcttgtg ttatttactt gtttaatctg 3600 ttcatactgt caaatataat ctgcatgttc tgaagcgtga tgtcgtgaca tccggtacga 3660 catctgtcat tggtatcaga atttcatgct gcaaatattt acaatagacc tcctcaacct 3720 caacagcaaa atcaaccaca gcagaacaat tatgacctct ccagcaacag atacaaccct 3780 ggatggagga atcaccctaa cctcagatgg tccagccctc agcaacaaca acagcagcct 3840 gctccttcct tccaaaatgc tgttggccca agcagaccat acattcctcc accaatccaa 3900 caacagcaac aaccccagaa acagccaaca gttgaggccc tccacaactt ccttcgaaga 3960 acttgtgagg caaatgacta tgcagaacat gcagtttcag caagagacta gagcctccat 4020 tcagagctta accaatcaga tgggacaatt ggctacccaa ttgaatcaac aacagtccca 4080 gaattctgac aagttgcctt ctcaagctgt ccaaaatccc aaaaatgtca gtgccatttc 4140 attgaggtcg ggaaagcagt gtcaaggacc tcaacccgta gcaccttcct catctgcaaa 4200 tgaacctgcc aaacttcact ctac 4224 9 62 PRT Glycine max misc_feature ORF1 9 Ser Arg Pro Arg Ala Leu Ile Arg Leu Thr Ile Gly Arg Arg Leu Asp 1 5 10 15 Leu Val Asp Asp Lys Val Ile Thr Leu Glu His Val Asp Thr Glu Glu 20 25 30 Gln Ile Ala Asp Ile Phe Thr Lys Ala Leu Asp Ala Asn Gln Phe Glu 35 40 45 Lys Leu Arg Gly Lys Leu Gly Ile Cys Leu Leu Glu Asp Leu 50 55 60 10 579 PRT Glycine max 10 Thr Leu Ile Ala Arg Ser Leu Leu Gly Gln Asn Lys Phe Asp Arg Cys 1 5 10 15 Phe Thr Arg Pro Ser Thr Phe Leu Ile Gln Thr His Ile Phe Val Val 20 25 30 Ile Ser Phe Ser Ala Phe Pro Asn Ser Ser Gln Arg Phe Thr Lys Pro 35 40 45 Phe Gln Arg Leu Cys Phe Ser Met Ala Thr Ser Pro Lys Asp Thr Ser 50 55 60 Ser Pro Gly Ser Pro Ser Val Pro Ser Ser Pro Ser Ser Thr Lys Ala 65 70 75 80 Pro Ser Asn Gln Glu Gln Pro Glu Phe His Ile Gln Pro Ile Gln Met 85 90 95 Ile Pro Gly Leu Ala Pro Val Pro Glu Lys Leu Val Pro Ile Arg Gln 100 105 110 Gln Gly Val Lys Ile Ser Glu Asn Pro Ser Ile Ala Thr Ser Pro Arg 115 120 125 Glu Leu Thr Arg Glu Met Asp Lys Lys Ile Arg Ser Ile Val Ser Ser 130 135 140 Ile Leu Lys Asn Ala Ser Val Pro Asp Ala Asp Lys Asp Val Pro Thr 145 150 155 160 Ser Ser Thr Pro Asn Ala Glu Val Leu Ser Ser Ser Ser Lys Glu Glu 165 170 175 Ser Thr Glu Glu Glu Glu Gln Ala Thr Glu Glu Thr Pro Ala Pro Arg 180 185 190 Ala Pro Glu Pro Ala Pro Gly Asp Leu Ile Asp Leu Glu Glu Val Glu 195 200 205 Ser Asp Glu Glu Pro Ile Ala Asn Lys Leu Ala Pro Gly Ile Ala Glu 210 215 220 Arg Leu Gln Ser Arg Lys Gly Lys Thr Pro Ile Thr Arg Ser Gly Arg 225 230 235 240 Ile Lys Thr Met Ala Gln Lys Lys Ser Thr Pro Ile Thr Pro Thr Thr 245 250 255 Ser Arg Trp Ser Lys Val Ala Ile Pro Ser Lys Lys Arg Lys Glu Phe 260 265 270 Ser Ser Ser Asp Ser Asp Asp Asp Val Glu Leu Asp Val Pro Asp Ile 275 280 285 Lys Arg Ala Lys Lys Ser Gly Lys Lys Val Pro Gly Asn Val Pro Asp 290 295 300 Ala Pro Leu Asp Asn Ile Ser Phe His Ser Ile Gly Asn Val Glu Arg 305 310 315 320 Trp Lys Phe Val Tyr Gln Arg Arg Leu Ala Leu Glu Arg Glu Leu Gly 325 330 335 Arg Asp Ala Leu Asp Cys Lys Glu Ile Met Asp Leu Ile Lys Gly Cys 340 345 350 Trp Thr Ala Glu Asn Ser His Gln Val Gly Arg Cys Tyr Glu Ser Leu 355 360 365 Val Arg Glu Phe Ile Val Asn Ile Pro Ser Asp Ile Thr Asn Arg Lys 370 375 380 Ser Asp Glu Tyr Gln Lys Val Phe Val Arg Gly Lys Cys Val Arg Phe 385 390 395 400 Ser Pro Ala Val Ile Asn Lys Tyr Leu Gly Arg Pro Thr Glu Gly Val 405 410 415 Val Asp Ile Ala Val Ser Glu His Gln Ile Ala Lys Glu Ile Thr Ala 420 425 430 Lys Gln Val Gln His Trp Pro Lys Lys Gly Lys Leu Ser Ala Gly Lys 435 440 445 Leu Ser Val Lys Tyr Ala Ile Leu His Arg Ile Gly Ala Ala Asn Trp 450 455 460 Val Pro Thr Asn His Thr Ser Thr Val Ala Thr Gly Leu Gly Lys Phe 465 470 475 480 Leu Tyr Ala Val Gly Thr Lys Ser Lys Phe Asn Phe Gly Lys Tyr Ile 485 490 495 Phe Asp Gln Thr Val Lys His Ser Glu Ser Phe Ala Val Lys Leu Pro 500 505 510 Ile Ala Phe Pro Thr Val Leu Cys Gly Ile Met Leu Ser Gln His Pro 515 520 525 Asn Ile Leu Asn Asn Ile Asp Ser Val Met Lys Lys Glu Ser Ala Leu 530 535 540 Ser Leu His Tyr Lys Leu Phe Glu Gly Thr His Val Pro Asp Ile Val 545 550 555 560 Ser Thr Ser Gly Lys Ala Ala Ala Ser Gly Ala Val Ser Lys Gly Cys 565 570 575 Phe Asp Cys 11 62 PRT Glycine max 11 Ser Arg Pro Arg Ala Leu Ile Arg Leu Thr Ile Gly Arg Arg Leu Asp 1 5 10 15 Leu Val Asp Asp Lys Val Ile Thr Leu Glu His Val Asp Thr Glu Glu 20 25 30 Gln Ile Ala Asp Ile Phe Thr Lys Ala Leu Asp Ala Asn Gln Phe Glu 35 40 45 Lys Leu Arg Gly Lys Leu Gly Ile Cys Leu Leu Glu Asp Leu 50 55 60 12 23 DNA Artificial Sequence primer 12 cccagtcacg acgttgtaaa acg 23 13 19 DNA Artificial Sequence primer 13 tcctttaagt tcagagatt 19 14 23 DNA Artificial Sequence primer 14 agcggataac aatttcacac agg 23 15 24 DNA Artificial Sequence primer 15 gtaatggtca accagaccac agtt 24 16 17 DNA Artificial Sequence primer 16 gacgaattgg cacttgg 17 17 18 DNA Artificial Sequence primer 17 tttgcactgc cttgggag 18 18 17 DNA Artificial Sequence primer 18 ccaaggagca caactgc 17 19 20 DNA Artificial Sequence primer 19 gctgaacaga atggacagga 20 20 19 DNA Artificial Sequence primer 20 aaagatataa caagattta 19 21 20 DNA Artificial Sequence primer 21 cccgatctta ttccttgaca 20 22 18 DNA Artificial Sequence primer 22 cttgccacag tagtgaca 18 23 18 DNA Artificial Sequence primer 23 tcttcccaag ctgtagca 18 24 19 DNA Artificial Sequence primer 24 tcctttaagt tcagagatt 19 25 20 DNA Artificial Sequence primer 25 agcgcgttct ctactgggcc 20 26 20 DNA Artificial Sequence primer 26 ccaccaaagc accatcaaac 20 27 20 DNA Artificial Sequence primer 27 ggcacagaag aagagcacac 20 28 20 DNA Artificial Sequence primer 28 tgcaaggaga tcatggacct 20 29 20 DNA Artificial Sequence primer 29 cacaggattg gcgctgcaaa 20 30 29 DNA Artificial Sequence primer 30 tccctggctt ggtagccccc agatgtagg 29 31 21 DNA Artificial Sequence primer 31 ggccctccac aacttccttc g 21 32 20 DNA Artificial Sequence primer 32 cagatgagga aggtgctacg 20 33 30 DNA Artificial Sequence primer 33 cccagttcgg tgcaacctca cctacatctg 30 34 20 DNA Artificial Sequence primer 34 ggtggctcac aaaacactca 20 35 20 DNA Artificial Sequence primer 35 tgtgtccagt attttcgggc 20 36 20 DNA Artificial Sequence primer 36 tcatcagata ctactccccc 20 37 22 DNA Artificial Sequence primer 37 cctaggactt gttgcaatgc ta 22 38 20 DNA Artificial Sequence primer 38 atgaggaatg tagagggacg 20 39 20 DNA Artificial Sequence primer 39 ctcatgagtt ctctgcagcc 20 40 29 DNA Artificial Sequence primer 40 gacaatgttg cagatacagc taaaagtgc 29 41 20 DNA Artificial Sequence primer 41 ccagatggat gtgaagagcg 20 42 19 DNA Artificial Sequence primer 42 tgggatggaa aatgccagc 19 43 20 DNA Artificial Sequence primer 43 agaactgtgt gtccctatcc 20 44 20 DNA Artificial Sequence primer 44 cctcagtgtc aacatgctcc 20 45 20 DNA Artificial Sequence primer 45 atcccatagt cactggtgcc 20 46 20 DNA Artificial Sequence primer 46 ctctgttagc ctttcatacc 20 47 20 DNA Artificial Sequence primer 47 cttgatcttg tagtgactcc 20 48 20 DNA Artificial Sequence primer 48 atacagtgtg gttggagtcc 20 49 20 DNA Artificial Sequence primer 49 gaagtcttag actcaactcc 20 50 2826 DNA Glycine max misc_feature SIRE-1 genomic clone 50 gatgaaggat tcaatgtaga cttcacagag tcagaatgct tgatgacaaa agagaagaga 60 gaagtcctaa tgaagggcgg cagatcaaag gacaactgtt acctgtggac acctcaagaa 120 accagttact cctccacatg tctattctcc aaagaagatg aagtcaaaat atggcatcaa 180 agatttggac atctgcactt aggaggcatg aagaaaatca ttgacaaagg tgctgttaga 240 ggcattccca atctgaaaat agaagaaggc agaatctgtg gtgaatgtca gattggaaag 300 caagtcaaga tgtccaacca gaagcttcaa catcagacca cttccagggt gctggaacta 360 cttcacatgg acttgatggg gcctatgcaa gttgaaagcc ttggaagaaa aaggtatgcc 420 tatgttgttg tggatgattt ctccagattt acctgggtca actttatcag agagaaatca 480 gacacctttg aagtattcaa ggagttgagt ctaagacttc aaagagaaaa agactgtgtc 540 atcaagagaa tcaggagtga ccatggcaga gagtttgaaa acagcaagtt tactgaattc 600 tgcacatctg aaggcatcac tcatgagttc tctgcagcca ttacaccaca acaaaatggc 660 atagttgaaa ggaaaaacag gaccttgcca gaagctgcta gggtcatgct tcatgccaaa 720 gaacttccct ataatctctg ggctgaagcc atgaacacag catgctacat ccacaacaga 780 gtcacactta gaagagggac tccaaccaca ctgtatgaaa tctggaaagg gaggaagcca 840 actgtcaagc acttccacat ctgtggaagt ccatgttaca ttttggcaga tagagagcaa 900 aggagaaaga tggatcccaa gagtgatgca gggatattct tgggatactc tacaaacagc 960 agagcatata gagtattcaa ttccagaacc agaactgtga tggaatccat caatgtggtt 1020 gttgatgatc taactccagc aagaaagaag gatgtcgaag aagatgtcag aacatcggga 1080 gacaatgttg cagatacagc taaaagtgca gaaaatgcag aaaactctga ttctgctaca 1140 gatgaaccaa acatcaatca acctgacaag agaccctcca ttagaatcca gaagatgcac 1200 cccaaggagc tgattatagg agatccaaac agaggagtca ctacaagatc aagggagatt 1260 gagattatct ccaattcatg ttttgtctcc aaaattgagc ccaagaatgt gaaagaggca 1320 ctgactgatg agttctggat caatgctatg caagaagaat tggagcaatt caaaaggaat 1380 gaagtttggg agctagttcc taggcccgag ggaactaatg tgattggcac caagtggatc 1440 ttcaagaaca aaaccaatga agaaggtgtt ataaccagaa acaaggccag acttgttgct 1500 caaggctaca ctcagattga aggtgtagac tttgatgaaa cttttgcccc tggtgctaaa 1560 cttgagtcca tcagactgtt acttggtgta gcttgcatcc tcaaattcaa gctgtaccag 1620 atggatgtga agagcgcatt tctgaatgga tacctgaatg aagaagccta tgtggagcag 1680 ccaaagggat ttgtagatcc aactcatcca gatcatgtat acaggctcaa gaagctctgc 1740 tatggattga agcaagcttc aagagcttgg tatgaaaggc taacagagtt ccttactcag 1800 caagggtata ggaagggggg gattgacaag accctttttg ttaaacaaga tgctggaaaa 1860 ttgatgatag cacagatata tgttgatgac attgtgtttg gagggatgtt gaatgagatg 1920 cttcgacatt ttgtccaaca gatgcaattt gaatttgaga tgagttttgt tggagagctg 1980 aattattttt tgggaatcca agtgaagcag atggaagaat ccatattcct ttcacaaagc 2040 aagtatgcaa agaacattgt caagaagttt gggatggaaa atgccagcca taaaagaaca 2100 cctgcaccta atcaattgaa gctgtcaaaa gatgaagctg gcaccagtgt tgatcaaagt 2160 ttgtacagaa gcatgattgg gagcttaata tatttaacag ctagcagacc tgacatcacc 2220 tatgcagtag gtggttgtgc aagatatcaa gccaatccta agataagtca cttgaatcaa 2280 gtaaagagaa ttttgaaata tgtaaatggc accagtgact atgggattat gtactgtcat 2340 tgttcagatt caatgctggt tgggtattgt gatgctgatt gggctggaag tgtagatgac 2400 agaaaaagca cttttggtgg atgtttttat ttgggaacca attttatttc atggttcagc 2460 aagaagcaga actgtgtgtc cctatccact gcagaagcag agtatattgc agcaggaagc 2520 agctgttcac aactagtttg gatgaagcag atgctcaagg agtacaatgt cgaacaagat 2580 gtcatgacat tgtactgtga caacttgagt gctattaata tttctaaaaa tcctgttcaa 2640 cacagcagaa ccaagcacat tgacattaga catcactata ttagagatct tgttgatgat 2700 aaagttatca cactggagca tgttgacact gaggaacaaa tagcagatat tttcacaaag 2760 gcattggatg caaatcagtt tgaaaaactg aggggcaagc tgggcatttg tctgctagag 2820 gattta 2826 51 942 PRT Glycine max 51 Asp Glu Gly Phe Asn Val Asp Phe Thr Glu Ser Glu Cys Leu Met Thr 1 5 10 15 Lys Glu Lys Arg Glu Val Leu Met Lys Gly Gly Arg Ser Lys Asp Asn 20 25 30 Cys Tyr Leu Trp Thr Pro Gln Glu Thr Ser Tyr Ser Ser Thr Cys Leu 35 40 45 Phe Ser Lys Glu Asp Glu Val Lys Ile Trp His Gln Arg Phe Gly His 50 55 60 Leu His Leu Gly Gly Met Lys Lys Ile Ile Asp Lys Gly Ala Val Arg 65 70 75 80 Gly Ile Pro Asn Leu Lys Ile Glu Glu Gly Arg Ile Cys Gly Glu Cys 85 90 95 Gln Ile Gly Lys Gln Val Lys Met Ser Asn Gln Lys Leu Gln His Gln 100 105 110 Thr Thr Ser Arg Val Leu Glu Leu Leu His Met Asp Leu Met Gly Pro 115 120 125 Met Gln Val Glu Ser Leu Gly Arg Lys Arg Tyr Ala Tyr Val Val Val 130 135 140 Asp Asp Phe Ser Arg Phe Thr Trp Val Asn Phe Ile Arg Glu Lys Ser 145 150 155 160 Asp Thr Phe Glu Val Phe Lys Glu Leu Ser Leu Arg Leu Gln Arg Glu 165 170 175 Lys Asp Cys Val Ile Lys Arg Ile Arg Ser Asp His Gly Arg Glu Phe 180 185 190 Glu Asn Ser Lys Phe Thr Glu Phe Cys Thr Ser Glu Gly Ile Thr His 195 200 205 Glu Phe Ser Ala Ala Ile Thr Pro Gln Gln Asn Gly Ile Val Glu Arg 210 215 220 Lys Asn Arg Thr Leu Pro Glu Ala Ala Arg Val Met Leu His Ala Lys 225 230 235 240 Glu Leu Pro Tyr Asn Leu Trp Ala Glu Ala Met Asn Thr Ala Cys Tyr 245 250 255 Ile His Asn Arg Val Thr Leu Arg Arg Gly Thr Pro Thr Thr Leu Tyr 260 265 270 Glu Ile Trp Lys Gly Arg Lys Pro Thr Val Lys His Phe His Ile Cys 275 280 285 Gly Ser Pro Cys Tyr Ile Leu Ala Asp Arg Glu Gln Arg Arg Lys Met 290 295 300 Asp Pro Lys Ser Asp Ala Gly Ile Phe Leu Gly Tyr Ser Thr Asn Ser 305 310 315 320 Arg Ala Tyr Arg Val Phe Asn Ser Arg Thr Arg Thr Val Met Glu Ser 325 330 335 Ile Asn Val Val Val Asp Asp Leu Thr Pro Ala Arg Lys Lys Asp Val 340 345 350 Glu Glu Asp Val Arg Thr Ser Gly Asp Asn Val Ala Asp Thr Ala Lys 355 360 365 Ser Ala Glu Asn Ala Glu Asn Ser Asp Ser Ala Thr Asp Glu Pro Asn 370 375 380 Ile Asn Gln Pro Asp Lys Arg Pro Ser Ile Arg Ile Gln Lys Met His 385 390 395 400 Pro Lys Glu Leu Ile Ile Gly Asp Pro Asn Arg Gly Val Thr Thr Arg 405 410 415 Ser Arg Glu Ile Glu Ile Ile Ser Asn Ser Cys Phe Val Ser Lys Ile 420 425 430 Glu Pro Lys Asn Val Lys Glu Ala Leu Thr Asp Glu Phe Trp Ile Asn 435 440 445 Ala Met Gln Glu Glu Leu Glu Gln Phe Lys Arg Asn Glu Val Trp Glu 450 455 460 Leu Val Pro Arg Pro Glu Gly Thr Asn Val Ile Gly Thr Lys Trp Ile 465 470 475 480 Phe Lys Asn Lys Thr Asn Glu Glu Gly Val Ile Thr Arg Asn Lys Ala 485 490 495 Arg Leu Val Ala Gln Gly Tyr Thr Gln Ile Glu Gly Val Asp Phe Asp 500 505 510 Glu Thr Phe Ala Pro Gly Ala Lys Leu Glu Ser Ile Arg Leu Leu Leu 515 520 525 Gly Val Ala Cys Ile Leu Lys Phe Lys Leu Tyr Gln Met Asp Val Lys 530 535 540 Ser Ala Phe Leu Asn Gly Tyr Leu Asn Glu Glu Ala Tyr Val Glu Gln 545 550 555 560 Pro Lys Gly Phe Val Asp Pro Thr His Pro Asp His Val Tyr Arg Leu 565 570 575 Lys Lys Leu Cys Tyr Gly Leu Lys Gln Ala Ser Arg Ala Trp Tyr Glu 580 585 590 Arg Leu Thr Glu Phe Leu Thr Gln Gln Gly Tyr Arg Lys Gly Gly Ile 595 600 605 Asp Lys Thr Leu Phe Val Lys Gln Asp Ala Gly Lys Leu Met Ile Ala 610 615 620 Gln Ile Tyr Val Asp Asp Ile Val Phe Gly Gly Met Leu Asn Glu Met 625 630 635 640 Leu Arg His Phe Val Gln Gln Met Gln Phe Glu Phe Glu Met Ser Phe 645 650 655 Val Gly Glu Leu Asn Tyr Phe Leu Gly Ile Gln Val Lys Gln Met Glu 660 665 670 Glu Ser Ile Phe Leu Ser Gln Ser Lys Tyr Ala Lys Asn Ile Val Lys 675 680 685 Lys Phe Gly Met Glu Asn Ala Ser His Lys Arg Thr Pro Ala Pro Asn 690 695 700 Gln Leu Lys Leu Ser Lys Asp Glu Ala Gly Thr Ser Val Asp Gln Ser 705 710 715 720 Leu Tyr Arg Ser Met Ile Gly Ser Leu Ile Tyr Leu Thr Ala Ser Arg 725 730 735 Pro Asp Ile Thr Tyr Ala Val Gly Gly Cys Ala Arg Tyr Gln Ala Asn 740 745 750 Pro Lys Ile Ser His Leu Asn Gln Val Lys Arg Ile Leu Lys Tyr Val 755 760 765 Asn Gly Thr Ser Asp Tyr Gly Ile Met Tyr Cys His Cys Ser Asp Ser 770 775 780 Met Leu Val Gly Tyr Cys Asp Ala Asp Trp Ala Gly Ser Val Asp Asp 785 790 795 800 Arg Lys Ser Thr Phe Gly Gly Cys Phe Tyr Leu Gly Thr Asn Phe Ile 805 810 815 Ser Trp Phe Ser Lys Lys Gln Asn Cys Val Ser Leu Ser Thr Ala Glu 820 825 830 Ala Glu Tyr Ile Ala Ala Gly Ser Ser Cys Ser Gln Leu Val Trp Met 835 840 845 Lys Gln Met Leu Lys Glu Tyr Asn Val Glu Gln Asp Val Met Thr Leu 850 855 860 Tyr Cys Asp Asn Leu Ser Ala Ile Asn Ile Ser Lys Asn Pro Val Gln 865 870 875 880 His Ser Arg Thr Lys His Ile Asp Ile Arg His His Tyr Ile Arg Asp 885 890 895 Leu Val Asp Asp Lys Val Ile Thr Leu Glu His Val Asp Thr Glu Glu 900 905 910 Gln Ile Ala Asp Ile Phe Thr Lys Ala Leu Asp Ala Asn Gln Phe Glu 915 920 925 Lys Leu Arg Gly Lys Leu Gly Ile Cys Leu Leu Glu Asp Leu 930 935 940 52 400 PRT Glycine max 52 Asp Glu Gly Phe Asn Val Asp Phe Thr Glu Ser Glu Cys Leu Met Thr 1 5 10 15 Lys Glu Lys Arg Glu Val Leu Met Lys Gly Gly Arg Ser Lys Asp Asn 20 25 30 Cys Tyr Leu Trp Thr Pro Gln Glu Thr Ser Tyr Ser Ser Thr Cys Leu 35 40 45 Phe Ser Lys Glu Asp Glu Val Lys Ile Trp His Gln Arg Phe Gly His 50 55 60 Leu His Leu Gly Gly Met Lys Lys Ile Ile Asp Lys Gly Ala Val Arg 65 70 75 80 Gly Ile Pro Asn Leu Lys Ile Glu Glu Gly Arg Ile Cys Gly Glu Cys 85 90 95 Gln Ile Gly Lys Gln Val Lys Met Ser Asn Gln Lys Leu Gln His Gln 100 105 110 Thr Thr Ser Arg Val Leu Glu Leu Leu His Met Asp Leu Met Gly Pro 115 120 125 Met Gln Val Glu Ser Leu Gly Arg Lys Arg Tyr Ala Tyr Val Val Val 130 135 140 Asp Asp Phe Ser Arg Phe Thr Trp Val Asn Phe Ile Arg Glu Lys Ser 145 150 155 160 Asp Thr Phe Glu Val Phe Lys Glu Leu Ser Leu Arg Leu Gln Arg Glu 165 170 175 Lys Asp Cys Val Ile Lys Arg Ile Arg Ser Asp His Gly Arg Glu Phe 180 185 190 Glu Asn Ser Lys Phe Thr Glu Phe Cys Thr Ser Glu Gly Ile Thr His 195 200 205 Glu Phe Ser Ala Ala Ile Thr Pro Gln Gln Asn Gly Ile Val Glu Arg 210 215 220 Lys Asn Arg Thr Leu Pro Glu Ala Ala Arg Val Met Leu His Ala Lys 225 230 235 240 Glu Leu Pro Tyr Asn Leu Trp Ala Glu Ala Met Asn Thr Ala Cys Tyr 245 250 255 Ile His Asn Arg Val Thr Leu Arg Arg Gly Thr Pro Thr Thr Leu Tyr 260 265 270 Glu Ile Trp Lys Gly Arg Lys Pro Thr Val Lys His Phe His Ile Cys 275 280 285 Gly Ser Pro Cys Tyr Ile Leu Ala Asp Arg Glu Gln Arg Arg Lys Met 290 295 300 Asp Pro Lys Ser Asp Ala Gly Ile Phe Leu Gly Tyr Ser Thr Asn Ser 305 310 315 320 Arg Ala Tyr Arg Val Phe Asn Ser Arg Thr Arg Thr Val Met Glu Ser 325 330 335 Ile Asn Val Val Val Asp Asp Leu Thr Pro Ala Arg Lys Lys Asp Val 340 345 350 Glu Glu Asp Val Arg Thr Ser Gly Asp Asn Val Ala Asp Thr Ala Lys 355 360 365 Ser Ala Glu Asn Ala Glu Asn Ser Asp Ser Ala Thr Asp Glu Pro Asn 370 375 380 Ile Asn Gln Pro Asp Lys Arg Pro Ser Ile Arg Ile Gln Lys Met His 385 390 395 400 53 381 PRT Glycine max 53 Pro Lys Glu Leu Ile Ile Gly Asp Pro Asn Arg Gly Val Thr Thr Arg 1 5 10 15 Ser Arg Glu Ile Glu Ile Ile Ser Asn Ser Cys Phe Val Ser Lys Ile 20 25 30 Glu Pro Lys Asn Val Lys Glu Ala Leu Thr Asp Glu Phe Trp Ile Asn 35 40 45 Ala Met Gln Glu Glu Leu Glu Gln Phe Lys Arg Asn Glu Val Trp Glu 50 55 60 Leu Val Pro Arg Pro Glu Gly Thr Asn Val Ile Gly Thr Lys Trp Ile 65 70 75 80 Phe Lys Asn Lys Thr Asn Glu Glu Gly Val Ile Thr Arg Asn Lys Ala 85 90 95 Arg Leu Val Ala Gln Gly Tyr Thr Gln Ile Glu Gly Val Asp Phe Asp 100 105 110 Glu Thr Phe Ala Pro Gly Ala Lys Leu Glu Ser Ile Arg Leu Leu Leu 115 120 125 Gly Val Ala Cys Ile Leu Lys Phe Lys Leu Tyr Gln Met Asp Val Lys 130 135 140 Ser Ala Phe Leu Asn Gly Tyr Leu Asn Glu Glu Ala Tyr Val Glu Gln 145 150 155 160 Pro Lys Gly Phe Val Asp Pro Thr His Pro Asp His Val Tyr Arg Leu 165 170 175 Lys Lys Leu Cys Tyr Gly Leu Lys Gln Ala Ser Arg Ala Trp Tyr Glu 180 185 190 Arg Leu Thr Glu Phe Leu Thr Gln Gln Gly Tyr Arg Lys Gly Gly Ile 195 200 205 Asp Lys Thr Leu Phe Val Lys Gln Asp Ala Gly Lys Leu Met Ile Ala 210 215 220 Gln Ile Tyr Val Asp Asp Ile Val Phe Gly Gly Met Leu Asn Glu Met 225 230 235 240 Leu Arg His Phe Val Gln Gln Met Gln Phe Glu Phe Glu Met Ser Phe 245 250 255 Val Gly Glu Leu Asn Tyr Phe Leu Gly Ile Gln Val Lys Gln Met Glu 260 265 270 Glu Ser Ile Phe Leu Ser Gln Ser Lys Tyr Ala Lys Asn Ile Val Lys 275 280 285 Lys Phe Gly Met Glu Asn Ala Ser His Lys Arg Thr Pro Ala Pro Asn 290 295 300 Gln Leu Lys Leu Ser Lys Asp Glu Ala Gly Thr Ser Val Asp Gln Ser 305 310 315 320 Leu Tyr Arg Ser Met Ile Gly Ser Leu Ile Tyr Leu Thr Ala Ser Arg 325 330 335 Pro Asp Ile Thr Tyr Ala Val Gly Gly Cys Ala Arg Tyr Gln Ala Asn 340 345 350 Pro Lys Ile Ser His Leu Asn Gln Val Lys Arg Ile Leu Lys Tyr Val 355 360 365 Asn Gly Thr Ser Asp Tyr Gly Ile Met Tyr Cys His Cys 370 375 380 54 166 PRT Glycine max SITE (162)..(162) X= any amino acid 54 Ser Asp Ser Met Leu Val Gly Tyr Cys Asp Ala Asp Trp Ala Gly Ser 1 5 10 15 Val Asp Asp Arg Lys Ser Thr Phe Gly Gly Cys Phe Tyr Leu Gly Thr 20 25 30 Asn Phe Ile Ser Trp Phe Ser Lys Lys Gln Asn Cys Val Ser Leu Ser 35 40 45 Thr Ala Glu Ala Glu Tyr Ile Ala Ala Gly Ser Ser Cys Ser Gln Leu 50 55 60 Val Trp Met Lys Gln Met Leu Lys Glu Tyr Asn Val Glu Gln Asp Val 65 70 75 80 Met Thr Leu Tyr Cys Asp Asn Leu Ser Ala Ile Asn Ile Ser Lys Asn 85 90 95 Pro Val Gln His Ser Arg Thr Lys His Ile Asp Ile Arg His His Tyr 100 105 110 Ile Arg Asp Leu Val Asp Asp Lys Val Ile Thr Leu Glu His Val Asp 115 120 125 Thr Glu Glu Gln Ile Ala Asp Ile Phe Thr Lys Ala Leu Asp Ala Asn 130 135 140 Gln Phe Glu Lys Leu Arg Gly Lys Leu Gly Ile Cys Leu Leu Glu Asp 145 150 155 160 Leu Xaa Asn Pro Xaa Pro 165 55 613 PRT Glycine max 55 Thr Leu Ile Ala Arg Ser Leu Leu Gly Gln Asn Lys Phe Asp Arg Cys 1 5 10 15 Phe Thr Arg Pro Ser Thr Phe Leu Ile Gln Thr His Ile Phe Val Val 20 25 30 Ile Ser Phe Ser Ala Phe Pro Asn Ser Ser Gln Arg Phe Thr Lys Pro 35 40 45 Phe Gln Arg Leu Cys Phe Ser Met Ala Thr Ser Pro Lys Asp Thr Ser 50 55 60 Ser Pro Gly Ser Pro Ser Val Pro Ser Ser Pro Ser Ser Thr Lys Ala 65 70 75 80 Pro Ser Asn Gln Glu Gln Pro Glu Phe His Ile Gln Pro Ile Gln Met 85 90 95 Ile Pro Gly Leu Ala Pro Val Pro Glu Lys Leu Val Pro Ile Arg Gln 100 105 110 Gln Gly Val Lys Ile Ser Glu Asn Pro Ser Ile Ala Thr Ser Pro Arg 115 120 125 Glu Leu Thr Arg Glu Met Asp Lys Lys Ile Arg Ser Ile Val Ser Ser 130 135 140 Ile Leu Lys Asn Ala Ser Val Pro Asp Ala Asp Lys Asp Val Pro Thr 145 150 155 160 Ser Ser Thr Pro Asn Ala Glu Val Leu Ser Ser Ser Ser Lys Glu Glu 165 170 175 Ser Thr Glu Glu Glu Glu Gln Ala Thr Glu Glu Thr Pro Ala Pro Arg 180 185 190 Ala Pro Glu Pro Ala Pro Gly Asp Leu Ile Asp Leu Glu Glu Val Glu 195 200 205 Ser Asp Glu Glu Pro Ile Ala Asn Lys Leu Ala Pro Gly Ile Ala Glu 210 215 220 Arg Leu Gln Ser Arg Lys Gly Lys Thr Pro Ile Thr Arg Ser Gly Arg 225 230 235 240 Ile Lys Thr Met Ala Gln Lys Lys Ser Thr Pro Ile Thr Pro Thr Thr 245 250 255 Ser Arg Trp Ser Lys Val Ala Ile Pro Ser Lys Lys Arg Lys Glu Phe 260 265 270 Ser Ser Ser Asp Ser Asp Asp Asp Val Glu Leu Asp Val Pro Asp Ile 275 280 285 Lys Arg Ala Lys Lys Ser Gly Lys Lys Val Pro Gly Asn Val Pro Asp 290 295 300 Ala Pro Leu Asp Asn Ile Ser Phe His Ser Ile Gly Asn Val Glu Arg 305 310 315 320 Trp Lys Phe Val Tyr Gln Arg Arg Leu Ala Leu Glu Arg Glu Leu Gly 325 330 335 Arg Asp Ala Leu Asp Cys Lys Glu Ile Met Asp Leu Ile Lys Gly Cys 340 345 350 Trp Thr Ala Glu Asn Ser His Gln Val Gly Arg Cys Tyr Glu Ser Leu 355 360 365 Val Arg Glu Phe Ile Val Asn Ile Pro Ser Asp Ile Thr Asn Arg Lys 370 375 380 Ser Asp Glu Tyr Gln Lys Val Phe Val Arg Gly Lys Cys Val Arg Phe 385 390 395 400 Ser Pro Ala Val Ile Asn Lys Tyr Leu Gly Arg Pro Thr Glu Gly Val 405 410 415 Val Asp Ile Ala Val Ser Glu His Gln Ile Ala Lys Glu Ile Thr Ala 420 425 430 Lys Gln Val Gln His Trp Pro Lys Lys Gly Lys Leu Ser Ala Gly Lys 435 440 445 Leu Ser Val Lys Tyr Ala Ile Leu His Arg Ile Gly Ala Ala Asn Trp 450 455 460 Val Pro Thr Asn His Thr Ser Thr Val Ala Thr Gly Leu Gly Lys Phe 465 470 475 480 Leu Tyr Ala Val Gly Thr Lys Ser Lys Phe Asn Phe Gly Lys Tyr Ile 485 490 495 Phe Asp Gln Thr Val Lys His Ser Glu Ser Phe Ala Val Lys Leu Pro 500 505 510 Ile Ala Phe Pro Thr Val Leu Cys Gly Ile Met Leu Ser Gln His Pro 515 520 525 Asn Ile Leu Asn Asn Ile Asp Ser Val Met Lys Lys Glu Ser Ala Leu 530 535 540 Ser Leu His Tyr Lys Leu Phe Glu Gly Thr His Val Pro Asp Ile Val 545 550 555 560 Ser Thr Ser Gly Lys Ala Ala Ala Ser Gly Ala Val Ser Lys Gly Cys 565 570 575 Phe Asp Cys Thr Gln Gly His Met Gln Gly Ala Gly Ser Asn His Gln 580 585 590 Ser His His Arg Lys Lys Asn Gly Ala Gly Thr Pro Asp Gln Lys Thr 595 600 605 Leu Arg Gln Trp His 610 56 183 DNA Glycine max 56 gttgctgcac aatgcacaag gcaagataaa agaagtgaag ctgcaggatc cacgatgtcg 60 gatacgatgt ccaagacatc tggcccgaaa atactggaca cataaatctg ttatatcttt 120 aacagattat tgtgcagtta gcaacaggtt agacgatcta tctttaggaa cgaactcttc 180 tag 183 57 138 DNA Glycine max 57 gacttcgtta tgtcaaggaa taagatcggg ctgcacaatg cacaaggcaa gataaaatgt 60 caaatgaaga attgaagctg caggatccat gatgtcggat acaatgtcca ggacatcctg 120 cccgaaaata ctggagtt 138 58 220 DNA Glycine max 58 tccaacgtta tgtcaaggaa tcagattggg ctccacaatg cacaaggcaa gataaaaggt 60 caaatgaaga attgaagctg caggatccac gatgtcggat acaatgtcca ggacatcctg 120 cccgaaaata ctggacacat aaatctgtta tatctttaac agattaatgt gcagttagca 180 acagatttgg cgatctatct ttaggaacga attaaaagat 220 59 579 PRT Glycine max 59 Thr Leu Ile Ala Arg Ser Leu Leu Gly Gln Asn Lys Phe Asp Arg Cys 1 5 10 15 Phe Thr Arg Pro Ser Thr Phe Leu Ile Gln Thr His Ile Phe Val Val 20 25 30 Ile Ser Phe Ser Ala Phe Pro Asn Ser Ser Gln Arg Phe Thr Lys Pro 35 40 45 Phe Gln Arg Leu Cys Phe Ser Met Ala Thr Ser Pro Lys Asp Thr Ser 50 55 60 Ser Pro Gly Ser Pro Ser Val Pro Ser Ser Pro Ser Ser Thr Lys Ala 65 70 75 80 Pro Ser Asn Gln Glu Gln Pro Glu Phe His Ile Gln Pro Ile Gln Met 85 90 95 Ile Pro Gly Leu Ala Pro Val Pro Glu Lys Leu Val Pro Ile Arg Gln 100 105 110 Gln Gly Val Lys Ile Ser Glu Asn Pro Ser Ile Ala Thr Ser Pro Arg 115 120 125 Glu Leu Thr Arg Glu Met Asp Lys Lys Ile Arg Ser Ile Val Ser Ser 130 135 140 Ile Leu Lys Asn Ala Ser Val Pro Asp Ala Asp Lys Asp Val Pro Thr 145 150 155 160 Ser Ser Thr Pro Asn Ala Glu Val Leu Ser Ser Ser Ser Lys Glu Glu 165 170 175 Ser Thr Glu Glu Glu Glu Gln Ala Thr Glu Glu Thr Pro Ala Pro Arg 180 185 190 Ala Pro Glu Pro Ala Pro Gly Asp Leu Ile Asp Leu Glu Glu Val Glu 195 200 205 Ser Asp Glu Glu Pro Ile Ala Asn Lys Leu Ala Pro Gly Ile Ala Glu 210 215 220 Arg Leu Gln Ser Arg Lys Gly Lys Thr Pro Ile Thr Arg Ser Gly Arg 225 230 235 240 Ile Lys Thr Met Ala Gln Lys Lys Ser Thr Pro Ile Thr Pro Thr Thr 245 250 255 Ser Arg Trp Ser Lys Val Ala Ile Pro Ser Lys Lys Arg Lys Glu Phe 260 265 270 Ser Ser Ser Asp Ser Asp Asp Asp Val Glu Leu Asp Val Pro Asp Ile 275 280 285 Lys Arg Ala Lys Lys Ser Gly Lys Lys Val Pro Gly Asn Val Pro Asp 290 295 300 Ala Pro Leu Asp Asn Ile Ser Phe His Ser Ile Gly Asn Val Glu Arg 305 310 315 320 Trp Lys Phe Val Tyr Gln Arg Arg Leu Ala Leu Glu Arg Glu Leu Gly 325 330 335 Arg Asp Ala Leu Asp Cys Lys Glu Ile Met Asp Leu Ile Lys Gly Cys 340 345 350 Trp Thr Ala Glu Asn Ser His Gln Val Gly Arg Cys Tyr Glu Ser Leu 355 360 365 Val Arg Glu Phe Ile Val Asn Ile Pro Ser Asp Ile Thr Asn Arg Lys 370 375 380 Ser Asp Glu Tyr Gln Lys Val Phe Val Arg Gly Lys Cys Val Arg Phe 385 390 395 400 Ser Pro Ala Val Ile Asn Lys Tyr Leu Gly Arg Pro Thr Glu Gly Val 405 410 415 Val Asp Ile Ala Val Ser Glu His Gln Ile Ala Lys Glu Ile Thr Ala 420 425 430 Lys Gln Val Gln His Trp Pro Lys Lys Gly Lys Leu Ser Ala Gly Lys 435 440 445 Leu Ser Val Lys Tyr Ala Ile Leu His Arg Ile Gly Ala Ala Asn Trp 450 455 460 Val Pro Thr Asn His Thr Ser Thr Val Ala Thr Gly Leu Gly Lys Phe 465 470 475 480 Leu Tyr Ala Val Gly Thr Lys Ser Lys Phe Asn Phe Gly Lys Tyr Ile 485 490 495 Phe Asp Gln Thr Val Lys His Ser Glu Ser Phe Ala Val Lys Leu Pro 500 505 510 Ile Ala Phe Pro Thr Val Leu Cys Gly Ile Met Leu Ser Gln His Pro 515 520 525 Asn Ile Leu Asn Asn Ile Asp Ser Val Met Lys Lys Glu Ser Ala Leu 530 535 540 Ser Leu His Tyr Lys Leu Phe Glu Gly Thr His Val Pro Asp Ile Val 545 550 555 560 Ser Thr Ser Gly Lys Ala Ala Ala Ser Gly Ala Val Ser Lys Gly Cys 565 570 575 Phe Asp Cys 60 14 PRT Artificial Sequence synthetic 60 Cys Xaa Xaa Cys Xaa Xaa Xaa Xaa His Xaa Xaa Xaa Xaa Cys 1 5 10 61 14 PRT Glycine max 61 Cys His Tyr Cys Gly Lys Tyr Gly His Ile Lys Pro Phe Cys 1 5 10 62 14 PRT Lilium henryi 62 Cys Tyr Ser Cys Gly Gln Pro Gly His Phe Lys Ala Asn Cys 1 5 10 63 14 PRT Drosophila melanogaster 63 Cys His His Cys Gly Arg Glu Gly His Ile Lys Lys Asp Cys 1 5 10 64 14 PRT Arabidopsis thaliana 64 Cys Trp Tyr Cys Lys Lys Glu Gly His Val Lys Lys Asp Cys 1 5 10 65 14 PRT Nicotiana tabacum 65 Cys Tyr Asn Cys Val Lys Pro Gly His Phe Lys Arg Asp Cys 1 5 10 66 14 PRT HIV-1 66 Cys Trp Lys Cys Gly Lys Pro Gly His Ile Met Thr Asn Cys 1 5 10 67 14 PRT Solanum tuberosum 67 Cys Asp His Cys Lys Lys Tyr Trp His Thr Arg Glu Thr Cys 1 5 10 68 14 PRT Cauliflower mosaic 68 Cys Trp Ile Cys Asn Ile Glu Gly His Tyr Ala Asn Glu Cys 1 5 10 69 10 PRT Arabidopsis thaliana 69 Leu Asp Ser Gly Cys Thr Ser His Met Ser 1 5 10 70 10 PRT Nicotiana tabacum 70 Val Asp Thr Ala Ala Ser His His Ala Thr 1 5 10 71 10 PRT Drosophila melanogaster 71 Leu Asp Ser Gly Ala Ser Asp His Leu Thr 1 5 10 72 10 PRT Solanum tuberosum 72 Ile Asp Ser Arg Ala Ser Asp His Met Thr 1 5 10 73 10 PRT Lilium henryi 73 Ile Asp Thr Gly Ser Thr His Ser Phe Ile 1 5 10 74 10 PRT Cauliflower mosaic 74 Val Asp Thr Gly Ala Ser Leu Cys Ile Ala 1 5 10 75 10 PRT HIV-1 75 Leu Asp Thr Gly Arg Asp Asp Thr Val Leu 1 5 10 76 22 RNA Glycine max misc_feature 3′-end of soybean tRNA met-1 (sequence is identified in the 5′ to 3′ direction in the sequence listing and in the 3′ to 5′ direction in Figure 11) 76 ucgaaaccug gcucugauac ca 22 77 20 DNA Solanum tuberosum 77 ttgcagtatc taaactttca 20 78 65 PRT Drosophila melanogaster 78 His Lys Arg Ala Lys His Ile Asp Ile Lys Tyr His Phe Ala Arg Glu 1 5 10 15 Gln Val Gln Asn Asn Val Ile Cys Leu Glu Tyr Ile Pro Thr Glu Asn 20 25 30 Gln Leu Ala Asp Ile Phe Thr Lys Pro Leu Pro Ala Ala Arg Phe Val 35 40 45 Glu Leu Arg Asp Lys Leu Gly Leu Leu Gln Asp Asp Gln Ser Asn Ala 50 55 60 Glu 65 79 441 PRT Zea mays SITE (1)..(441) amino acid positions 86-526 of Opie-2 retroelement 79 Asn Met Gly Tyr Asn Cys Leu Phe Thr Asn Ile Asp Val Ser Val Phe 1 5 10 15 Arg Arg Cys Asp Gly Ser Leu Ala Phe Lys Gly Val Leu Asp Gly Lys 20 25 30 Leu Tyr Leu Val Asp Phe Ala Lys Glu Glu Ala Gly Leu Asp Ala Cys 35 40 45 Leu Ile Ala Lys Thr Ser Met Gly Trp Leu Trp His Arg Arg Leu Ala 50 55 60 His Val Gly Met Lys Asn Leu His Lys Leu Leu Lys Gly Glu His Val 65 70 75 80 Ile Gly Leu Thr Asn Val Gln Phe Glu Lys Asp Arg Pro Cys Ala Ala 85 90 95 Cys Gln Ala Gly Lys Gln Val Gly Gly Ser His His Thr Lys Asn Val 100 105 110 Met Thr Thr Ser Arg Pro Leu Glu Met Leu His Met Asp Leu Phe Gly 115 120 125 Pro Val Ala Tyr Leu Ser Ile Gly Gly Ser Lys Tyr Gly Leu Val Ile 130 135 140 Val Asp Asp Phe Ser Arg Phe Thr Trp Val Phe Phe Leu Gln Glu Lys 145 150 155 160 Ser Glu Thr Gln Gly Thr Leu Lys Arg Phe Leu Arg Arg Ala Gln Asn 165 170 175 Glu Phe Glu Leu Lys Val Lys Lys Ile Arg Ser Asp Asn Gly Ser Glu 180 185 190 Phe Lys Asn Leu Gln Val Glu Glu Phe Leu Glu Glu Glu Gly Ile Lys 195 200 205 His Glu Phe Ser Ala Pro Tyr Thr Pro Gln Gln Asn Gly Val Val Glu 210 215 220 Arg Lys Asn Arg Thr Leu Ile Asp Met Ala Arg Thr Met Leu Gly Glu 225 230 235 240 Phe Lys Thr Pro Glu Cys Phe Trp Thr Glu Ala Val Asn Thr Ala Cys 245 250 255 His Ala Ile Asn Arg Val Tyr Leu His Arg Ile Leu Lys Asn Thr Ser 260 265 270 Tyr Glu Leu Leu Thr Gly Asn Lys Pro Asn Val Ser Tyr Phe Arg Val 275 280 285 Phe Gly Ser Lys Cys Tyr Ile Leu Val Lys Lys Gly Arg Asn Ser Lys 290 295 300 Phe Ala Pro Lys Ala Val Glu Gly Phe Leu Leu Gly Tyr Asp Ser Asn 305 310 315 320 Thr Lys Ala Tyr Arg Val Phe Asn Lys Ser Ser Gly Leu Val Glu Val 325 330 335 Ser Gly Asp Val Val Phe Asp Glu Thr Asn Gly Ser Pro Arg Glu Gln 340 345 350 Val Val Asp Cys Asp Asp Val Asp Glu Glu Asp Ile Pro Thr Ala Ala 355 360 365 Ile Arg Thr Met Ala Ile Gly Glu Val Arg Pro Gln Glu Gln Asp Glu 370 375 380 Arg Glu Gln Pro Ser Pro Ser Thr Met Val His Pro Pro Thr Gln Asp 385 390 395 400 Asp Glu Gln Val His Gln Gln Glu Val Cys Asp Gln Gly Gly Ala Gln 405 410 415 Asp Asp His Val Leu Glu Glu Glu Ala Gln Pro Ala Pro Pro Thr Gln 420 425 430 Val Arg Ala Met Ile Gln Arg Asp His 435 440 80 380 PRT Zea mays SITE (1)..(380) amino acid positions 527-906 of Opie-2 retroelement 80 Pro Val Asp Gln Ile Leu Gly Asp Ile Ser Lys Gly Val Thr Thr Arg 1 5 10 15 Ser Arg Leu Val Asn Phe Cys Glu His Asn Ser Phe Val Ser Ser Ile 20 25 30 Glu Pro Phe Arg Val Glu Glu Ala Leu Leu Asp Pro Asp Trp Val Leu 35 40 45 Ala Met Gln Glu Glu Leu Asn Asn Phe Lys Arg Asn Glu Val Trp Thr 50 55 60 Leu Val Pro Arg Pro Lys Gln Asn Val Val Gly Thr Lys Trp Val Phe 65 70 75 80 Arg Asn Lys Gln Asp Glu Arg Gly Val Val Thr Arg Asn Lys Ala Arg 85 90 95 Leu Val Ala Lys Gly Tyr Ala Gln Val Ala Gly Leu Asp Phe Glu Glu 100 105 110 Thr Phe Ala Pro Val Ala Arg Leu Glu Ser Ile Arg Ile Leu Leu Ala 115 120 125 Tyr Ala Ala His His Ser Phe Arg Leu Tyr Gln Met Asp Val Lys Ser 130 135 140 Ala Phe Leu Asn Gly Pro Ile Lys Glu Glu Val Tyr Val Glu Gln Pro 145 150 155 160 Pro Gly Phe Glu Asp Glu Arg Tyr Pro Asp His Val Cys Lys Leu Ser 165 170 175 Lys Ala Leu Tyr Gly Leu Lys Gln Ala Pro Arg Ala Trp Tyr Glu Cys 180 185 190 Leu Arg Asp Phe Leu Ile Ala Asn Ala Phe Lys Val Gly Lys Ala Asp 195 200 205 Pro Thr Leu Phe Thr Lys Thr Cys Asp Gly Asp Leu Phe Val Cys Gln 210 215 220 Ile Tyr Val Asp Asp Ile Ile Phe Gly Ser Thr Asn Gln Lys Ser Cys 225 230 235 240 Glu Glu Phe Ser Arg Val Met Thr Gln Lys Phe Glu Met Ser Met Met 245 250 255 Gly Glu Leu Asn Tyr Phe Leu Gly Phe Gln Val Lys Gln Leu Lys Asp 260 265 270 Gly Thr Phe Ile Ser Gln Thr Lys Tyr Thr Gln Asp Leu Leu Lys Arg 275 280 285 Phe Gly Met Lys Asp Ala Lys Pro Ala Lys Thr Pro Met Gly Thr Asp 290 295 300 Gly His Thr Asp Leu Asn Lys Gly Gly Lys Ser Val Asp Gln Lys Ala 305 310 315 320 Tyr Arg Ser Met Ile Gly Ser Leu Leu Tyr Leu Cys Ala Ser Arg Pro 325 330 335 Asp Ile Met Leu Ser Val Cys Met Cys Ala Arg Phe Gln Ser Asp Pro 340 345 350 Lys Glu Cys His Leu Val Ala Val Lys Arg Ile Leu Arg Tyr Leu Val 355 360 365 Ala Thr Pro Cys Phe Gly Leu Trp Tyr Pro Lys Gly 370 375 380 81 168 PRT Zea mays SITE (1)..(168) nucleotide positions 901-1068 of Opie-2 nucleotide sequence 81 Leu Trp Tyr Pro Lys Gly Ser Thr Phe Asp Leu Val Gly Tyr Ser Asp 1 5 10 15 Ser Asp Tyr Ala Gly Cys Lys Val Asp Arg Lys Ser Thr Ser Gly Thr 20 25 30 Cys Gln Phe Leu Gly Arg Ser Leu Val Ser Trp Asn Ser Lys Lys Gln 35 40 45 Thr Ser Val Ala Leu Ser Thr Ala Glu Ala Glu Tyr Val Ala Ala Gly 50 55 60 Gln Cys Cys Ala Gln Leu Leu Trp Met Arg Gln Thr Leu Arg Asp Phe 65 70 75 80 Gly Tyr Asn Leu Ser Lys Val Pro Leu Leu Cys Asp Asn Glu Ser Ala 85 90 95 Ile Arg Met Ala Glu Asn Pro Val Glu His Ser Arg Thr Lys His Ile 100 105 110 Asp Ile Arg His His Phe Leu Arg Asp His Gln Gln Lys Gly Asp Ile 115 120 125 Glu Val Phe His Val Ser Thr Glu Asn Gln Leu Ala Asp Ile Phe Thr 130 135 140 Lys Pro Leu Asp Glu Lys Thr Phe Cys Arg Leu Arg Ser Glu Leu Asn 145 150 155 160 Val Leu Asp Ser Arg Asn Leu Asp 165 82 4 PRT Artificial Sequence synthetic 82 Lys Lys Gly Lys 1 83 647 PRT Glycine max 83 Thr Leu Ile Ala Arg Ser Leu Leu Gly Gln Asn Lys Phe Asp Arg Cys 1 5 10 15 Phe Thr Arg Pro Ser Thr Phe Leu Ile Gln Thr His Ile Phe Val Val 20 25 30 Ile Ser Phe Ser Ala Phe Pro Asn Ser Ser Gln Arg Phe Thr Lys Pro 35 40 45 Phe Gln Arg Leu Cys Phe Ser Met Ala Thr Ser Pro Lys Asp Thr Ser 50 55 60 Ser Pro Gly Ser Pro Ser Val Pro Ser Ser Pro Ser Ser Thr Lys Ala 65 70 75 80 Pro Ser Asn Gln Glu Gln Pro Glu Phe His Ile Gln Pro Ile Gln Met 85 90 95 Ile Pro Gly Gln Ala Pro Val Pro Glu Lys Leu Val Pro Lys Arg Gln 100 105 110 Gln Gly Val Lys Ile Ser Glu Asn Pro Ser Ile Ala Thr Ser Pro Arg 115 120 125 Val Asp Thr Glu Met Asp Lys Lys Ile Arg Ser Ile Val Ser Ser Ile 130 135 140 Leu Lys Asn Ala Ser Val Pro Asp Ala Asp Lys Asp Val Pro Thr Ser 145 150 155 160 Ser Thr Pro Asn Ala Glu Val Leu Ser Ser Ser Ser Lys Glu Glu Ser 165 170 175 Thr Glu Glu Glu Glu Gln Ala Thr Glu Glu Thr Pro Ala Pro Arg Ala 180 185 190 Pro Glu Pro Ala Pro Gly Asp Leu Ile Asp Leu Glu Glu Val Glu Ser 195 200 205 Asp Glu Glu Pro Ile Ala Asn Lys Leu Ala Pro Gly Ile Ala Glu Arg 210 215 220 Leu Gln Ser Arg Lys Gly Lys Thr Pro Ile Thr Arg Ser Gly Arg Ile 225 230 235 240 Lys Thr Met Ala Gln Lys Lys Ser Thr Pro Ile Thr Pro Thr Thr Ser 245 250 255 Arg Trp Ser Lys Val Ala Ile Pro Ser Lys Lys Arg Lys Glu Phe Ser 260 265 270 Ser Ser Asp Ser Asp Asp Asp Val Glu Leu Asp Val Pro Asp Ile Lys 275 280 285 Arg Ala Lys Lys Ser Gly Lys Lys Val Pro Gly Asn Val Pro Asp Ala 290 295 300 Pro Leu Asp Asn Ile Ser Phe His Ser Ile Gly Asn Val Glu Arg Trp 305 310 315 320 Lys Phe Val Tyr Gln Arg Arg Leu Ala Leu Glu Arg Glu Leu Gly Arg 325 330 335 Asp Ala Leu Asp Cys Lys Glu Ile Met Asp Leu Ile Lys Ala Ala Gly 340 345 350 Leu Leu Lys Thr Val Thr Lys Leu Gly Asp Cys Tyr Glu Ser Leu Val 355 360 365 Arg Glu Phe Ile Val Asn Ile Pro Ser Asp Ile Thr Asn Arg Lys Ser 370 375 380 Asp Glu Tyr Gln Lys Val Phe Val Arg Gly Lys Cys Val Arg Phe Ser 385 390 395 400 Pro Ala Val Ile Asn Lys Tyr Leu Gly Arg Pro Thr Glu Gly Val Val 405 410 415 Asp Ile Ala Val Ser Glu His Gln Ile Ala Lys Glu Ile Thr Ala Lys 420 425 430 Gln Val Gln His Trp Pro Lys Lys Gly Lys Leu Ser Ala Gly Lys Leu 435 440 445 Ser Val Lys Tyr Ala Ile Leu His Arg Ile Gly Ala Ala Asn Trp Val 450 455 460 Pro Thr Asn His Thr Ser Thr Val Ala Thr Gly Leu Gly Lys Phe Leu 465 470 475 480 Tyr Ala Val Gly Thr Lys Ser Lys Phe Asn Phe Gly Lys Tyr Ile Phe 485 490 495 Asp Gln Thr Val Lys His Ser Glu Ser Phe Ala Val Lys Leu Pro Ile 500 505 510 Ala Phe Pro Thr Val Leu Cys Gly Ile Met Leu Ser Gln His Pro Asn 515 520 525 Ile Leu Asn Asn Ile Asp Ser Val Met Lys Arg Glu Ser Ala Leu Ser 530 535 540 Leu His Tyr Lys Leu Phe Glu Gly Thr His Val Pro Asp Ile Val Ser 545 550 555 560 Thr Ser Gly Lys Ala Ala Ala Ser Gly Ala Val Ser Lys Asp Ala Leu 565 570 575 Ile Ala Glu Leu Lys Asp Thr Cys Lys Val Leu Glu Ala Thr Ile Lys 580 585 590 Ala Thr Thr Glu Lys Lys Met Glu Leu Glu Arg Leu Ile Lys Arg Leu 595 600 605 Ser Asp Ser Gly Ile Asp Asp Gly Glu Ala Ala Glu Glu Glu Glu Glu 610 615 620 Ala Ala Glu Glu Glu Lys Asp Ala Ala Glu Asp Thr Glu Ser Asp Asp 625 630 635 640 Asp Asp Ser Asp Ala Thr Pro 645 84 578 PRT Glycine max 84 Thr Leu Ile Ala Arg Ser Leu Leu Gly Gln Asn Lys Phe Asp Arg Cys 1 5 10 15 Phe Thr Arg Pro Ser Thr Phe Leu Ile Gln Thr His Ile Phe Val Val 20 25 30 Ile Ser Phe Ser Ala Phe Pro Asn Ser Ser Gln Arg Phe Thr Lys Pro 35 40 45 Phe Gln Arg Leu Cys Phe Ser Met Ala Thr Ser Pro Lys Asp Thr Ser 50 55 60 Ser Pro Gly Ser Pro Ser Val Pro Ser Ser Pro Ser Ser Thr Lys Ala 65 70 75 80 Pro Ser Asn Gln Glu Gln Pro Glu Phe His Ile Gln Pro Ile Gln Met 85 90 95 Ile Pro Gly Leu Ala Pro Val Pro Glu Lys Leu Val Pro Ile Arg Gln 100 105 110 Gln Gly Val Lys Ile Ser Glu Asn Pro Ser Ile Ala Thr Ser Pro Arg 115 120 125 Glu Leu Thr Arg Glu Met Asp Lys Lys Ile Arg Ser Ile Val Ser Ser 130 135 140 Ile Leu Lys Asn Ala Ser Val Pro Asp Ala Asp Lys Asp Val Pro Thr 145 150 155 160 Ser Ser Thr Pro Asn Ala Glu Val Leu Ser Ser Ser Ser Lys Glu Glu 165 170 175 Ser Thr Glu Glu Glu Glu Gln Ala Thr Glu Glu Thr Pro Ala Pro Arg 180 185 190 Ala Pro Glu Pro Ala Pro Gly Asp Leu Ile Asp Leu Glu Glu Val Glu 195 200 205 Ser Asp Glu Glu Pro Ile Ala Asn Lys Leu Ala Pro Gly Ile Ala Glu 210 215 220 Arg Leu Gln Ser Arg Lys Gly Lys Thr Pro Ile Thr Arg Ser Gly Arg 225 230 235 240 Ile Lys Thr Met Ala Gln Lys Lys Ser Thr Pro Ile Thr Pro Thr Thr 245 250 255 Ser Arg Trp Ser Lys Val Ala Ile Pro Ser Lys Lys Arg Lys Glu Phe 260 265 270 Ser Ser Ser Asp Ser Asp Asp Asp Val Glu Leu Asp Val Pro Asp Ile 275 280 285 Lys Arg Ala Lys Lys Ser Gly Lys Lys Val Pro Gly Asn Val Pro Asp 290 295 300 Ala Pro Leu Asp Asn Ile Ser Phe His Ser Ile Gly Asn Val Glu Arg 305 310 315 320 Trp Lys Phe Val Tyr Gln Arg Arg Leu Ala Leu Glu Arg Glu Leu Gly 325 330 335 Arg Asp Ala Leu Asp Cys Lys Glu Ile Met Asp Leu Ile Lys Gly Cys 340 345 350 Trp Thr Ala Glu Asn Ser His Gln Val Gly Arg Cys Tyr Glu Ser Leu 355 360 365 Val Arg Glu Phe Ile Val Asn Ile Pro Ser Asp Ile Thr Asn Arg Lys 370 375 380 Ser Asp Glu Tyr Gln Lys Val Phe Val Arg Gly Lys Cys Val Arg Phe 385 390 395 400 Ser Pro Ala Val Ile Asn Lys Tyr Leu Gly Arg Pro Thr Glu Gly Val 405 410 415 Val Asp Ile Ala Val Ser Glu His Gln Ile Ala Lys Glu Ile Thr Ala 420 425 430 Gln Val Gln His Trp Pro Lys Lys Gly Lys Leu Ser Ala Gly Lys Leu 435 440 445 Ser Val Lys Tyr Ala Ile Leu His Arg Ile Gly Ala Ala Asn Trp Val 450 455 460 Pro Thr Asn His Thr Ser Thr Val Ala Thr Gly Leu Gly Lys Phe Leu 465 470 475 480 Tyr Ala Val Gly Thr Lys Ser Lys Phe Asn Phe Gly Lys Tyr Ile Phe 485 490 495 Asp Gln Thr Val Lys His Ser Glu Ser Phe Ala Val Lys Leu Pro Ile 500 505 510 Ala Phe Pro Pro Val Leu Cys Gly Ile Met Leu Thr Gln His Pro Asn 515 520 525 Ile Leu Asn Asn Ile Asp Ser Val Met Lys Lys Glu Ser Ala Leu Ser 530 535 540 Leu His Tyr Lys Leu Phe Glu Gly Thr His Val Pro Asp Ile Val Ser 545 550 555 560 Thr Ser Gly Lys Ala Ala Ala Ser Gly Ala Val Ser Lys Gly Cys Phe 565 570 575 Asp Cys 85 8 PRT Glycine max 85 Gln Leu Leu Leu Ser Glu Arg Ala 1 5 86 34 PRT Glycine max 86 Thr Gln Gly His Met Gln Gly Ala Gly Ser Asn His Gln Ser His His 1 5 10 15 Arg Lys Lys Asn Gly Ala Gly Thr Pro Asp Gln Lys Thr Leu Arg Gln 20 25 30 Trp His 

I claim:
 1. An isolated, purified polynucleotide comprising a polynucleotide selected from the group consisting of SEQ ID NO:3, SEQ ID NO:8, SEQ ID NO:50, polynucleotides that hybridize under stringent conditions to any one of the foregoing polynucleotides and that have the properties of the foregoing polynucleotides, and fragments thereof, wherein said fragments retain the properties of their respective parent polynucleotides.
 2. The polynucleotide of claim 1 wherein said fragments comprise all or part of one or more SIRE-1 long terminal repeats.
 3. The polynucleotide of claim 1 further comprising a heterologous DNA.
 4. The polynucleotide of claim 3 wherein said heterologous DNA comprises a transcriptional regulatory element.
 5. A vector comprising the polynucleotide according to claim
 1. 6. The vector of claim 5 further comprising a heterologous DNA.
 7. The vector of claim 6 wherein said heterologous DNA comprises a transcriptional regulatory element.
 8. The vector of claim 6 wherein said heterologous DNA is operably linked to a transcriptional regulatory element.
 9. The vector of claim 8 wherein the heterologous DNA comprises a DNA encoding a protein conferring resistance to a plant disease.
 10. The vector of claim 8 wherein said heterologous DNA comprises a DNA encoding a protein conferring resistance to insect infestation.
 11. The vector of claim 8 wherein said heterologous DNA comprises a DNA encoding a protein conferring tolerance to a herbicide.
 12. The vector of claim 8 wherein said heterologous DNA comprises a DNA encoding a protein conferring tolerance enhanced nitrogen fixation or nodulation.
 13. The vector of claim 8 wherein said heterologous DNA comprises a DNA encoding a protein conferring enhanced vigor or growth.
 14. The vector of claim 8 wherein said heterologous DNA comprises a DNA encoding a SIRE-1-encoded protein.
 15. The vector of claim 8 wherein said heterologous DNA comprises a gene or a fragment thereof.
 16. The vector of claim 8 wherein said heterologous DNA comprises a DNA encoding an antisense transcript.
 17. A method for transforming a host cell comprising the step of introducing a vector according to claim 5, or into said host cell.
 18. A host cell transformed by the method of claim
 17. 19. The host cell according to claim 18 wherein said host cell is a plant cell.
 20. A method for making a heterologous protein comprising the steps of: (a) culturing a host cell according to claim 18 under suitable medium and environmental conditions; and (b) isolating said protein from said cultured cell or from said medium.
 21. The host cell according to claim 19 wherein said plant cell is a soybean cell.
 22. An isolated, purified SIRE-1-encoded protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 59, SEQ ID NO: 83, SEQ ID NO: 84 and fragments thereof, wherein said protein fragments retain the properties of their respective parent proteins.
 23. The protein of claim 22, wherein said protein is a recombinant protein.
 24. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 59, SEQ ID NO:83, SEQ ID NO: 84 and fragments thereof.
 25. A method for transforming a plant cell, said method comprising the steps of: (a) introducing a polynucleotide according to claim 1 into a plant cell; and (b) culturing said plant cell under suitable nutrient and environmental conditions; and (c) detecting said polynucleotide in said plant cell.
 26. A method for transforming a plant cell, said method comprising the steps of: (a) introducing a vector according to any one of claims 5 to 8 into a plant cell; (b) culturing said plant cell under suitable nutrient and environmental conditions for the expression of an expression product of said polynucleotide; and (c) detecting said expression product.
 27. A transformed plant cell produced by the method of claim 25 claim
 26. 28. The transformed plant cell of claim 27 wherein said plant cell is a soybean cell.
 29. A transgenic plant comprising a vector according to claims 5, 6, 7, or
 8. 30. A method for generating a transgenic plant, the method comprising: (a) introducing a vector according to claim 6 into a plant cell and detecting the polynucleotide in the plant cell; and (b) generating a plant from the cell of step (a), wherein the plant comprises cells which contain the heterologous DNA.
 31. A transgenic plant produced according to the method of claim 30 or transgenic progeny thereof that contain the heterologous DNA.
 32. An isolated, purified SIRE-1-encoded protein comprising SEQ ID NO:
 10. 33. An isolated purified polynucleotide selected from the group consisting of: (a) SEQ ID NO: 3; and (b) DNA molecules that hybridize under stringent conditions to the complement of SEQ ID NO: 3, wherein said DNA molecules have the properties of SEQ ID NO:
 3. 34. An isolated purified polynucleotide selected from the group consisting of: (a) SEQ ID NO: 8; and (b) DNA molecules that hybridize under stringent conditions to the complement of SEQ ID NO: 8, wherein said DNA molecules have the properties of SEQ ID NO:
 8. 35. An isolated purified polynucleotide selected from the group consisting of: (a) SEQ ID NO: 50; and (b) DNA molecules that hybridize under stringent conditions to the complement of SEQ ID NO: 50, wherein said DNA molecules have the properties of SEQ ID NO:
 50. 36. An isolated, purified polynucleotide comprising the polynucleotide of SEQ ID NO:
 3. 37. An isolated, purified polynucleotide comprising the polynucleotide of SEQ ID NO:
 8. 38. An isolated, purified polynucleotide comprising the polynucleotide of SEQ ID NO:
 50. 39. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 10. 40. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 11. 41. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 51. 42. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 52. 43. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 53. 44. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 54. 45. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 55. 46. An isolated, purified SIRE-1-encoded protein comprising the amino acid sequence of SEQ ID NO:
 59. 47. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 10. 48. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 11. 49. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 51. 50. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 52. 51. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 53. 52. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 54. 53. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 55. 54. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 59. 55. An isolated, purified SIRE-1-encoded protein comprising an amino acid sequence of SEQ ID NO:
 83. 56. An isolated, purified SIRE-1-encoded protein comprising an amino acid sequence of SEQ ID NO:
 84. 57. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 83. 58. An isolated, purified antibody that specifically recognizes an epitope on a protein comprising an amino acid sequence of SEQ ID NO:
 84. 